SV calling using multiple software tools with results evaluated using the Jaccard Index Measure

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Description

Multi-stage Snakemake pipeline that combines python and BASH scripts for Structural Variant (SV) calling with multiple third-party long-read and assembly alignment-based SV calling tools. In addition, this pipeline evaluates all SV results produced based on their consistency with other tools using the Jacccard index measure and Truvari. This workflow simplifies the generation of a comprehensive evidence-based SV result set and to aid SV studies that require well-supported SV results.

Supported formats

SV-JIM requires genome assemblies from both a reference and query sample in FASTA format and a long-reads FASTQ file containing reads that belongs to query sample. The input genome assembly files must be pre-downloaded by the user and the path information must be updated in the configuration file prior to execution. Similarly, the read file can also be provided before execution; however, the pipeline also supports prefetching read data with SRATools based on the accession information added to the config file.

After execution, SV-JIM produces multiple SV result files in Variant Call Format (VCF), including the original outputs, intersections for specific tool combinations, and aggregated SV results on the basis of minimum supporting callers (Ex: minTwo or minThree).

Dependencies

SV-JIM is a Snakemake pipeline that utilizes multiple third party software tools. Many of these tools are installable as conda package so the pipeline includes a conda configuration file for user convenience.

The full list of required software is provided below and includes version information for the software versions that were used during testing:

Dependencies installed through the provided conda configuration file

  • biopython (1.80)

  • cutesv (2.0.2)

  • svim (1.4.2)

  • svim-asm (1.0.3)

  • intervaltree (3.0.2)

  • scipy (1.10.0)

  • mamba (1.2.0)

  • numpy (1.24.2)

  • snakemake (7.21.0)

  • pysam (0.20.0)

  • sniffles=2.0 (2.0.7)

  • pandas (1.5.3)

  • matplotlib (3.6.3)

  • matplotlib-venn (0.11.7)

  • truvari (3.5.0)

Other dependencies

  • SRA-Tools (3.0.2)

  • Minimap2 (2.24-r1122)

  • SAMTools (1.16.1)

  • BCFTools (1.16)

  • BEDTools (2.30.0)

  • PAV (2.2.1)

Additionally, the pipeline must be launched from an environment with Snakemake installed.

Installation

As a Snakemake workflow that employs external tools, the installation only involves cloning this repository: 

git clone https://github.com/CMalcolmTodd/SV-JIM

After cloning the SV-JIM repository, the conda dependencies will be loaded by Snakemake automatically during execution based on the included conda env configuration file. For the remaining dependencies please consult the installation instructions provided by each tool's github/manual and ensure these tools are added to your PATH variable.

Configuration

For configuration, SV-JIM provides a config file template used by Snakemake to specify the required input files, conda environments, options, and directory information to enable execution. The provided template config file features many default values that utilize the provided working directory structure; however, these values are configurable if the preference is to use alternative directories. Further details on each of the available parameters is provided in later in this section.

Finally, SV-JIM includes a conda environment file that permits Snakemake to install many of the pipeline's dependencies; however, the provided pipeline config file can also be updated to use alternative conda environment files if using separate conda environments with specific/non-conflicting software versions is required.

If an alternative conda environment is preferable, a conda environment file can be generated as follows: 

conda env export -n <condaEnvName> -f <fileName>.yaml --from-history

Any additional conda files created must be placed in the Rules directory to allow for access by Snakemake during execution and please provide updated file name information for each tool's conda file in the pipeline's config file.

Configuration file options:

Input File Configurations Section

Reference Sequence Information

  • refSampleName : Short ID for user to distinguish files (EX: "NI100")

  • refAssembly : Path to Reference Fenome fasta file (EX: "./Genomes/Bnigra_NI100.fasta")

  • refSeqsFile : File of regions in the reference genome to include. For example, the chromosomes only. (EX:"./Genomes/RefSeqsToInclude.txt")

    • Contents of the target file should contain one region per line.

    • This type of file can be created with:

      • grep ">[Chrom_Prefix]" [genomeFasta] | tr -d ">" > [refSeqListFile]
Query Sequence Information

  • qrySampleName : Short ID for user to distinguish files (EX: "C2")

  • qryAssembly : Path to Reference Fenome fasta file (EX: "./Genomes/Bnigra_NI100.fasta")

  • qrySeqsFile : File of regions/contigs in the query assembly to be included. (EX:"./Genomes/QrySeqsToInclude.txt")

    • Contents of the target file should contain one region per line.

    • This type of file can be created quickly with:

      • grep ">[Chrom_Prefix]" [genomeFasta] | tr -d ">" > [qrySeqListFile]
Read Input Information

  • readFilesList : "../Arabidopsis_Data/ReadAccessions.txt" # List of Accession numbers (one per line) for Long-reads to be included during execution (EX: "SRR11906206")

  • firstLRAccession : "ERR3415826" # Accession number for first file in the readFilesList (to check if requiring download from SRA)

Environment and Working Directory Configurations

Environment Information
  • threads : Desired number of threads to use during execution based on hardware available (EX: 30)
Working Directory Information

Default options can be created easily using the 'build-workspace.sh' script provided in home directory of this repo.

  • genomesFolder : Path to target directory containing the reference and query fasta files.

    • (EX: "./Genomes")

  • longReadsFolder : Path to target directory containing the long read data (in fastq) applicable to the query sample.

    • (EX: "./Long_Reads")

  • qualimapReportsFolder : Path to target directory into which Qualimap reports will be written.

    • (EX: "./Qualimap_Reports")

  • alignResultsFolder : Path to target directory into which minimap2 alignment results will be written.

    • (EX: "./Alignments")

  • svResultsFolder : Path to parent directory into which all SV caller results will be written.

    • (EX: "./SV_Calls")

  • intersectResultsFolder : Path to parent directory into which all BEDTools intersect results will be written.

    • (EX: "./Intersections")

  • truvariResultsFolder : Path to parent directory into which all Truvari bench results will be written.

    • (EX:"./Truvari_Results")

  • aggregatedResultsFolder : Path to parent directory into which SV results supported by a minimum number of SV callers for each tool will be written.

    • (EX:"./Aggregated_SV_Results")
Conda Environment Information

This repo includes a YAML env file provided that contains all conda related dependency programs for user convenience. Additionally, using a single environment file with all of the required software reduces pipeline execution time since snakemake will regenerate it's own copies of each environment automatically. However, the following separate options are available should the user require/prefer to use separate environments. Any YAML files to be used should be placed in the Rules subdirectory for Snakemake to access.

To use a single conda environment, please specify the same target YAML file for all five parameters.

  • cuteSVCondaEnvYAML : Path to YAML file for conda env that CuteSV is installed in. (EX: "All-Env.yaml")

  • sniffles2CondaEnvYAML : Path to YAML file for conda env that Sniffles2 is installed in. (EX: "All-Env.yaml")

  • svimCondaEnvYAML : Path to YAML file for conda env that SVIM is installed in. (EX:"All-Env.yaml")

  • svimASMCondaEnvYAML : Path to YAML file for conda env that SVIM-ASM is installed in. (EX: "All-Env.yaml")

  • pavCondaEnvYAML : Path to YAML file for conda environment with PAV dependencies installed. (EX: "All-Env.yaml")

Software Configurations

SRATools Configurations

For context, the default value provided is based on the size of the read data files used during initial testing

  • prefetchMaxSize : Maximum file size that will downloaded during prefetch operation. (EX: "50G")
Minimap2 Aligner Configurations (for more details see minimap2 --help)

For context, the default settings taken from the supplementary information of the orginal CuteSV and SVIM-ASM publications since these publications compared the performance of similar software that is used in the pipeline. Additional details and options for each setting can also be found in the minimap2 --help menu.

  • presetForLR : Predefined settings based on sequencing tech.

    • (EX: "map-ont" OR "map-pb" OR "map-hifi", etc.)

  • presetForAssemblies : Predefined settings for query assembly to ref alignment based on maximum allowable sequence divergence.

    • (EX: asm5 OR asm10 OR asm20)

  • minimapZDropForLR : Z drop score and Inversion Z drop score parameter in minimap (EX: "600,200")

SAMTools Configurations

For context, these default settings were taken from the supplementary information from the original SVIM-ASM publication since this parameter value was successfully used in their testing.

  • memSettingForAssemblySort : Memory required for sorting minimap2's assembly-to-ref alignment output. (EX: "4G")
General SV Caller Configurations

For context, these default settings were taken from the supplementary information of the CuteSV publication since this publication demonstrated high quality performance rates when comparing the outputs of similar read-based SV Callers used in the pipeline.

  • minMAPQForSVs : PHRED-scaled quality score for the probability of error for an aligned base (EX: 20)

    • PHRED scores typically range from 4-60 with 10 representing 10% error, 20 representing 1%, 30 representing 0.1%, and 40 representing 0.01%

    • Additional details on PHRED-scaled quality scores can be found in the Phred-scaled quality scores article.

  • minSuppReadsForSVs : Min number of reads that support/indicate the presence of an SV. (EX: 10)

  • minSizeForSVs : Min size of SVs to be detected [50 is the common definition in literature]. (EX: 50)

  • maxSizeForSVs : Filtering maximum size for SV detectable by tools (EX: 300000)

CuteSV Configurations

As with the general SV configurations above, the default settings are taken from the CuteSV publication. Please see the CuteSV repo for more details on the significance of these settings.

  • maxClusterBias : 100

  • diffRatio : 0.3

Truvari Bench Configurations

Default settings inspired by thresholds used in published literature and in the SVIM-ASM publications' supplementary information. See truvari bench --help menu for more details on settings.

  • overlapThreshold : Rate of similarity required in the sizes of the SVs locations being compared. (EX: 0.5 [or 50% which is a commonly used threshold in literature])

  • maxRefDistance : Maximum distance (in number of bases) permitted when comparing the reference sequence index reported for the SV locations being compared (EX: 1000)

Pipeline Benchmarking Configurations

  • benchmarkDir: Path information for where to write benchmarking files.

    • (EX: "./Benchmarking")

  • repeatsForBench: Frequency for how many times to repeat a task as part of benchmarking. (EX: 1)

    • Note, increasing this parameter will significantly increase execution time. So unless benchmarking, recommended to be left at 1

Usage

A) Set Up/Pre-work

  1. Update the provided SV-JIM config file to reflect the target input sequence information and update any setting values you wish to change from the defaults

  2. Create the files for the refSeqsFile and qrySeqsFile to specify only the target genome/assembly chroms/contigs to be considered during the pipeline's execution

    • See grep command suggestion in the Configuration section above for assistance

  3. Create the file for the readFilesList to specify which read accessions are to be included during execution.

    • Note: If any of input read files cannot/won't be fetched from SRA, please preprocess the file name to ensure the read's fastq file is unzipped and renamed to '.fastq' to prevent unnecessary prefetching using SRATools.

B) Perform a dry run:

Recommended first step to confirm configuration/settings prior to executions. Performing a dry run (-np) Builds the directed acyclic graph representing the outstanding tasks of the workflow and prints the applicable commands to be run at each stage of pipeline to allow for review, but doesn't execute any of the related commands. Dry runs are also useful as they can identify errors that may occur based on current configurations and pre-work completed.

  1. cd to SV-JIM home directory

  2. Update configuration file to reflect inputs to be processed

  3. Run: snakemake -np

C) Execute SV-JIM once configuration is prepared:

Builds the directed acyclic graph representing the outstanding tasks of the workflow and begins execution of the underlying software. Note: the order of execution for the outstanding tasks can vary between executions.

  1. cd to SV-JIM home directory

  2. Run: snakemake --use-conda --cores <# threads>

Note:

  • Adding --rerun-incompletes to the command may be necessary if the pipeline terminates unexpectedly during execution to restart tasks that were in progress at the time.

  • Unexpected termination may also result in a locked working directory; however, this lock can be removed by either running snakemake --unlock in the SV-JIM home directory or by deleting the contents of the <PAV_Directory>/.snakemake/locks/ directory if the reported lock was applied by PAV's Snakemake pipeline.

Pipeline Test Example (Arabidopsis thaliana)

Input data

Due to size, the experiment's input sequence data should be obtained from the publicly accessible resources below:

Experiment set up

The provided config file should already contain many of the necessary configurations, but please make the following updates:

  1. Update the chromosome header information in the TAIR10 reference genome to be more concise/clear within the output and to match the Ler chrom IDs

    • Ex: change longer chromosome 1 header in TAIR10 to >chr1

    • Repeat for all chromosomes by searching for the '>' characters that begin each header

  2. Generate a RefSeqsToInclude.txt and QrySeqsToInclude.txt using the grep instructions in the Config section to identify the sequences to be included from both genomes.

  3. Unzip and rename the downloaded ERR3415826 reads FASTQ file to ERR3415826.fastq to be consistent with the config file value provided.

  4. Update provided config file's refAssembly , refSeqsFile , qryAssembly , and qrySeqsFile values to reflect the user's local path information for where the input data files are stored

Running the experiment

Once configured the pipeline can be executed similar to the usage instructions above:

  1. Run: snakemake --use-conda --cores <# threads>

Note: For additional execution stats, Snakemake supports a --stat <statsFile> if further execution statistics prove helpful to the user.

Known issues

List of current issues

Getting help

If you have questions, concerns, bug reports, etc, please file an issue in this repository's Issue Tracker or e-mail [email protected] .

Future work

Have suggestions on how the software can be improved? Please contact [email protected] with your suggestions/recommendations!

Current worklist:

  • Update Rules and Scripts to use zipped data inputs to improve memory footprint

  • Research parallelization options/caps for each tool and refine threads argument for each rule

  • Add Docstrings to Snakemake Rules files to improve internal documentation for users

MIT licensing info

  1. LICENSE

Code Snippets

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shell:
        "bash ./Scripts/align_reads_w_minimap2.sh {threads} {params.zDrop} {params.mnmp2Preset} {params.refGenome} {output} {params.alignOutDir} {params.readsDir} {input.readFilesList}"
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shell:
        "mkdir -p {params.svOutDir};\n"
        "svim-asm haploid --min_mapq {params.minMAPQ} --min_sv_size {params.minSize} --max_sv_size {params.maxSize} {params.svOutDir} {input.inputFile} {params.refGenome};"
        "mv {params.svOutDir}/variants.vcf {output}"
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        "mkdir -p {params.svOutDir};\n"
        "bash ./Scripts/run-PAV-SnakeMake-pipe.sh {threads} {params.svOutDir} {input} {params.qryID}"
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPCallALL} {params.callTPCallSSm} {params.callTPCallSml} {params.callTPCallMed} {params.callTPCallLrg};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPBaseALL} {params.callTPBaseSSm} {params.callTPBaseSml} {params.callTPBaseMed} {params.callTPBaseLrg};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.baseTPCallALL} {params.baseTPCallSSm} {params.baseTPCallSml} {params.baseTPCallMed} {params.baseTPCallLrg}"
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallSSm} {params.tpCallSml} {params.tpCallMed} {params.tpCallLrg};\n"
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        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallSSm} {params.tpCallSml} {params.tpCallMed} {params.tpCallLrg};\n"
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        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPBaseALL} {params.callTPBaseSSm} {params.callTPBaseSml} {params.callTPBaseMed} {params.callTPBaseLrg};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.baseTPCallALL} {params.baseTPCallSSm} {params.baseTPCallSml} {params.baseTPCallMed} {params.baseTPCallLrg}"
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        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPBaseALL} {params.callTPBaseSSm} {params.callTPBaseSml} {params.callTPBaseMed} {params.callTPBaseLrg};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.baseTPCallALL} {params.baseTPCallSSm} {params.baseTPCallSml} {params.baseTPCallMed} {params.baseTPCallLrg}"
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        "bash ./Scripts/combine_vcf_files_basic.sh {params.baseTPCallALL} {params.baseTPCallSSm} {params.baseTPCallSml} {params.baseTPCallMed} {params.baseTPCallLrg}"
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        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPBaseALL} {params.callTPBaseSSm} {params.callTPBaseSml} {params.callTPBaseMed} {params.callTPBaseLrg};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.baseTPCallALL} {params.baseTPCallSSm} {params.baseTPCallSml} {params.baseTPCallMed} {params.baseTPCallLrg}"
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        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
SnakeMake From line 82 of Rules/combine_types_vcfs_to_all_lrg.smk 
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        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
SnakeMake From line 103 of Rules/combine_types_vcfs_to_all_lrg.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPCallALL} {params.callTPCallDEL} {params.callTPCallINS} {params.callTPCallDUP} {params.callTPCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPBaseALL} {params.callTPBaseDEL} {params.callTPBaseINS} {params.callTPBaseDUP} {params.callTPBaseINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.baseTPCallALL} {params.baseTPCallDEL} {params.baseTPCallINS} {params.baseTPCallDUP} {params.baseTPCallINV}"
SnakeMake From line 152 of Rules/combine_types_vcfs_to_all_lrg.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallDUP} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseDUP} {params.tpBaseINV}"
SnakeMake From line 190 of Rules/combine_types_vcfs_to_all_lrg.smk 
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        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
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        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
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        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
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        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
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        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
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        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
SnakeMake From line 329 of Rules/combine_types_vcfs_to_all_lrg.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseINV}"
SnakeMake From line 361 of Rules/combine_types_vcfs_to_all_lrg.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseINV}"
SnakeMake From line 394 of Rules/combine_types_vcfs_to_all_lrg.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseINV}"
SnakeMake From line 427 of Rules/combine_types_vcfs_to_all_lrg.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseINV}"
SnakeMake From line 460 of Rules/combine_types_vcfs_to_all_lrg.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseINV}"
SnakeMake From line 493 of Rules/combine_types_vcfs_to_all_lrg.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseINV}"
SnakeMake From line 526 of Rules/combine_types_vcfs_to_all_lrg.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallDUP} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseDUP} {params.tpBaseINV}"
SnakeMake From line 563 of Rules/combine_types_vcfs_to_all_lrg.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallDUP} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseDUP} {params.tpBaseINV}"
SnakeMake From line 600 of Rules/combine_types_vcfs_to_all_lrg.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallDUP} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseDUP} {params.tpBaseINV}"
SnakeMake From line 639 of Rules/combine_types_vcfs_to_all_lrg.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPCallALL} {params.callTPCallDEL} {params.callTPCallINS} {params.callTPCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPBaseALL} {params.callTPBaseDEL} {params.callTPBaseINS} {params.callTPBaseINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.baseTPCallALL} {params.baseTPCallDEL} {params.baseTPCallINS} {params.baseTPCallINV}"
SnakeMake From line 683 of Rules/combine_types_vcfs_to_all_lrg.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPCallALL} {params.callTPCallDEL} {params.callTPCallINS} {params.callTPCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPBaseALL} {params.callTPBaseDEL} {params.callTPBaseINS} {params.callTPBaseINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.baseTPCallALL} {params.baseTPCallDEL} {params.baseTPCallINS} {params.baseTPCallINV}"
SnakeMake From line 728 of Rules/combine_types_vcfs_to_all_lrg.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPCallALL} {params.callTPCallDEL} {params.callTPCallINS} {params.callTPCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPBaseALL} {params.callTPBaseDEL} {params.callTPBaseINS} {params.callTPBaseINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.baseTPCallALL} {params.baseTPCallDEL} {params.baseTPCallINS} {params.baseTPCallINV}"
SnakeMake From line 773 of Rules/combine_types_vcfs_to_all_lrg.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPCallALL} {params.callTPCallDEL} {params.callTPCallINS} {params.callTPCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPBaseALL} {params.callTPBaseDEL} {params.callTPBaseINS} {params.callTPBaseINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.baseTPCallALL} {params.baseTPCallDEL} {params.baseTPCallINS} {params.baseTPCallINV}"
SnakeMake From line 820 of Rules/combine_types_vcfs_to_all_lrg.smk 
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        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
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        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
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        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
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        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
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        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
SnakeMake From line 103 of Rules/combine_types_vcfs_to_all_med.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPCallALL} {params.callTPCallDEL} {params.callTPCallINS} {params.callTPCallDUP} {params.callTPCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPBaseALL} {params.callTPBaseDEL} {params.callTPBaseINS} {params.callTPBaseDUP} {params.callTPBaseINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.baseTPCallALL} {params.baseTPCallDEL} {params.baseTPCallINS} {params.baseTPCallDUP} {params.baseTPCallINV}"
SnakeMake From line 152 of Rules/combine_types_vcfs_to_all_med.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallDUP} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseDUP} {params.tpBaseINV}"
SnakeMake From line 190 of Rules/combine_types_vcfs_to_all_med.smk 
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        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
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        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
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        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
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        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
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        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
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        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
SnakeMake From line 329 of Rules/combine_types_vcfs_to_all_med.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseINV}"
SnakeMake From line 361 of Rules/combine_types_vcfs_to_all_med.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseINV}"
SnakeMake From line 394 of Rules/combine_types_vcfs_to_all_med.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseINV}"
SnakeMake From line 427 of Rules/combine_types_vcfs_to_all_med.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseINV}"
SnakeMake From line 460 of Rules/combine_types_vcfs_to_all_med.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseINV}"
SnakeMake From line 493 of Rules/combine_types_vcfs_to_all_med.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseINV}"
SnakeMake From line 526 of Rules/combine_types_vcfs_to_all_med.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallDUP} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseDUP} {params.tpBaseINV}"
SnakeMake From line 563 of Rules/combine_types_vcfs_to_all_med.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallDUP} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseDUP} {params.tpBaseINV}"
SnakeMake From line 600 of Rules/combine_types_vcfs_to_all_med.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallDUP} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseDUP} {params.tpBaseINV}"
SnakeMake From line 639 of Rules/combine_types_vcfs_to_all_med.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPCallALL} {params.callTPCallDEL} {params.callTPCallINS} {params.callTPCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPBaseALL} {params.callTPBaseDEL} {params.callTPBaseINS} {params.callTPBaseINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.baseTPCallALL} {params.baseTPCallDEL} {params.baseTPCallINS} {params.baseTPCallINV}"
SnakeMake From line 683 of Rules/combine_types_vcfs_to_all_med.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPCallALL} {params.callTPCallDEL} {params.callTPCallINS} {params.callTPCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPBaseALL} {params.callTPBaseDEL} {params.callTPBaseINS} {params.callTPBaseINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.baseTPCallALL} {params.baseTPCallDEL} {params.baseTPCallINS} {params.baseTPCallINV}"
SnakeMake From line 728 of Rules/combine_types_vcfs_to_all_med.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPCallALL} {params.callTPCallDEL} {params.callTPCallINS} {params.callTPCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPBaseALL} {params.callTPBaseDEL} {params.callTPBaseINS} {params.callTPBaseINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.baseTPCallALL} {params.baseTPCallDEL} {params.baseTPCallINS} {params.baseTPCallINV}"
SnakeMake From line 773 of Rules/combine_types_vcfs_to_all_med.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPCallALL} {params.callTPCallDEL} {params.callTPCallINS} {params.callTPCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPBaseALL} {params.callTPBaseDEL} {params.callTPBaseINS} {params.callTPBaseINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.baseTPCallALL} {params.baseTPCallDEL} {params.baseTPCallINS} {params.baseTPCallINV}"
SnakeMake From line 820 of Rules/combine_types_vcfs_to_all_med.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
SnakeMake From line 19 of Rules/combine_types_vcfs_to_all_sml.smk 
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        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
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        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
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        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
SnakeMake From line 82 of Rules/combine_types_vcfs_to_all_sml.smk 
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        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
SnakeMake From line 103 of Rules/combine_types_vcfs_to_all_sml.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPCallALL} {params.callTPCallDEL} {params.callTPCallINS} {params.callTPCallDUP} {params.callTPCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPBaseALL} {params.callTPBaseDEL} {params.callTPBaseINS} {params.callTPBaseDUP} {params.callTPBaseINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.baseTPCallALL} {params.baseTPCallDEL} {params.baseTPCallINS} {params.baseTPCallDUP} {params.baseTPCallINV}"
SnakeMake From line 152 of Rules/combine_types_vcfs_to_all_sml.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallDUP} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseDUP} {params.tpBaseINV}"
SnakeMake From line 190 of Rules/combine_types_vcfs_to_all_sml.smk 
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        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
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        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
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        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
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        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
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        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
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        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
SnakeMake From line 329 of Rules/combine_types_vcfs_to_all_sml.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseINV}"
SnakeMake From line 361 of Rules/combine_types_vcfs_to_all_sml.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseINV}"
SnakeMake From line 394 of Rules/combine_types_vcfs_to_all_sml.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseINV}"
SnakeMake From line 427 of Rules/combine_types_vcfs_to_all_sml.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseINV}"
SnakeMake From line 460 of Rules/combine_types_vcfs_to_all_sml.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseINV}"
SnakeMake From line 493 of Rules/combine_types_vcfs_to_all_sml.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseINV}"
SnakeMake From line 526 of Rules/combine_types_vcfs_to_all_sml.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallDUP} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseDUP} {params.tpBaseINV}"
SnakeMake From line 563 of Rules/combine_types_vcfs_to_all_sml.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallDUP} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseDUP} {params.tpBaseINV}"
SnakeMake From line 600 of Rules/combine_types_vcfs_to_all_sml.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallDUP} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseDUP} {params.tpBaseINV}"
SnakeMake From line 639 of Rules/combine_types_vcfs_to_all_sml.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPCallALL} {params.callTPCallDEL} {params.callTPCallINS} {params.callTPCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPBaseALL} {params.callTPBaseDEL} {params.callTPBaseINS} {params.callTPBaseINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.baseTPCallALL} {params.baseTPCallDEL} {params.baseTPCallINS} {params.baseTPCallINV}"
SnakeMake From line 683 of Rules/combine_types_vcfs_to_all_sml.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPCallALL} {params.callTPCallDEL} {params.callTPCallINS} {params.callTPCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPBaseALL} {params.callTPBaseDEL} {params.callTPBaseINS} {params.callTPBaseINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.baseTPCallALL} {params.baseTPCallDEL} {params.baseTPCallINS} {params.baseTPCallINV}"
SnakeMake From line 728 of Rules/combine_types_vcfs_to_all_sml.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPCallALL} {params.callTPCallDEL} {params.callTPCallINS} {params.callTPCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPBaseALL} {params.callTPBaseDEL} {params.callTPBaseINS} {params.callTPBaseINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.baseTPCallALL} {params.baseTPCallDEL} {params.baseTPCallINS} {params.baseTPCallINV}"
SnakeMake From line 773 of Rules/combine_types_vcfs_to_all_sml.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPCallALL} {params.callTPCallDEL} {params.callTPCallINS} {params.callTPCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPBaseALL} {params.callTPBaseDEL} {params.callTPBaseINS} {params.callTPBaseINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.baseTPCallALL} {params.baseTPCallDEL} {params.baseTPCallINS} {params.baseTPCallINV}"
SnakeMake From line 820 of Rules/combine_types_vcfs_to_all_sml.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
SnakeMake From line 19 of Rules/combine_types_vcfs_to_all_ssm.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
SnakeMake From line 40 of Rules/combine_types_vcfs_to_all_ssm.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
SnakeMake From line 61 of Rules/combine_types_vcfs_to_all_ssm.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
SnakeMake From line 82 of Rules/combine_types_vcfs_to_all_ssm.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
SnakeMake From line 103 of Rules/combine_types_vcfs_to_all_ssm.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPCallALL} {params.callTPCallDEL} {params.callTPCallINS} {params.callTPCallDUP} {params.callTPCallINV} {params.callTPCallBND};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPBaseALL} {params.callTPBaseDEL} {params.callTPBaseINS} {params.callTPBaseDUP} {params.callTPBaseINV} {params.callTPBaseBND};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.baseTPCallALL} {params.baseTPCallDEL} {params.baseTPCallINS} {params.baseTPCallDUP} {params.baseTPCallINV} {params.baseTPCallBND}"
SnakeMake From line 158 of Rules/combine_types_vcfs_to_all_ssm.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallDUP} {params.tpCallINV} {params.tpCallBND};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseDUP} {params.tpBaseINV} {params.tpBaseBND}"
SnakeMake From line 200 of Rules/combine_types_vcfs_to_all_ssm.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
SnakeMake From line 226 of Rules/combine_types_vcfs_to_all_ssm.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
SnakeMake From line 251 of Rules/combine_types_vcfs_to_all_ssm.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
SnakeMake From line 276 of Rules/combine_types_vcfs_to_all_ssm.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
SnakeMake From line 301 of Rules/combine_types_vcfs_to_all_ssm.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
SnakeMake From line 326 of Rules/combine_types_vcfs_to_all_ssm.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params}"
SnakeMake From line 351 of Rules/combine_types_vcfs_to_all_ssm.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseINV}"
SnakeMake From line 383 of Rules/combine_types_vcfs_to_all_ssm.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseINV}"
SnakeMake From line 416 of Rules/combine_types_vcfs_to_all_ssm.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseINV}"
SnakeMake From line 449 of Rules/combine_types_vcfs_to_all_ssm.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseINV}"
SnakeMake From line 482 of Rules/combine_types_vcfs_to_all_ssm.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseINV}"
SnakeMake From line 515 of Rules/combine_types_vcfs_to_all_ssm.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseINV}"
SnakeMake From line 548 of Rules/combine_types_vcfs_to_all_ssm.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallDUP} {params.tpCallINV} {params.tpCallBND};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseDUP} {params.tpBaseINV} {params.tpBaseBND}"
SnakeMake From line 589 of Rules/combine_types_vcfs_to_all_ssm.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallDUP} {params.tpCallINV} {params.tpCallBND};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseDUP} {params.tpBaseINV} {params.tpBaseBND}"
SnakeMake From line 630 of Rules/combine_types_vcfs_to_all_ssm.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpCallALL} {params.tpCallDEL} {params.tpCallINS} {params.tpCallDUP} {params.tpCallINV} {params.tpCallBND};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.tpBaseALL} {params.tpBaseDEL} {params.tpBaseINS} {params.tpBaseDUP} {params.tpBaseINV} {params.tpBaseBND}"
SnakeMake From line 671 of Rules/combine_types_vcfs_to_all_ssm.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPCallALL} {params.callTPCallDEL} {params.callTPCallINS} {params.callTPCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPBaseALL} {params.callTPBaseDEL} {params.callTPBaseINS} {params.callTPBaseINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.baseTPCallALL} {params.baseTPCallDEL} {params.baseTPCallINS} {params.baseTPCallINV}"
SnakeMake From line 715 of Rules/combine_types_vcfs_to_all_ssm.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPCallALL} {params.callTPCallDEL} {params.callTPCallINS} {params.callTPCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPBaseALL} {params.callTPBaseDEL} {params.callTPBaseINS} {params.callTPBaseINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.baseTPCallALL} {params.baseTPCallDEL} {params.baseTPCallINS} {params.baseTPCallINV}"
SnakeMake From line 760 of Rules/combine_types_vcfs_to_all_ssm.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPCallALL} {params.callTPCallDEL} {params.callTPCallINS} {params.callTPCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPBaseALL} {params.callTPBaseDEL} {params.callTPBaseINS} {params.callTPBaseINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.baseTPCallALL} {params.baseTPCallDEL} {params.baseTPCallINS} {params.baseTPCallINV}"
SnakeMake From line 805 of Rules/combine_types_vcfs_to_all_ssm.smk 
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shell:
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPCallALL} {params.callTPCallDEL} {params.callTPCallINS} {params.callTPCallINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.callTPBaseALL} {params.callTPBaseDEL} {params.callTPBaseINS} {params.callTPBaseINV};\n"
        "bash ./Scripts/combine_vcf_files_basic.sh {params.baseTPCallALL} {params.baseTPCallDEL} {params.baseTPCallINS} {params.baseTPCallINV}"
SnakeMake From line 852 of Rules/combine_types_vcfs_to_all_ssm.smk 
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shell:
        "bash ./Scripts/aggregate_truvari_tp_files_no_dups.sh {params} {input}"
SnakeMake From line 15 of Rules/determine_sv_sets_min_callers.smk 
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shell:
        "bash ./Scripts/aggregate_truvari_tp_files_no_dups.sh {params} {input}"
SnakeMake From line 32 of Rules/determine_sv_sets_min_callers.smk 
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shell:
        "bash ./Scripts/aggregate_truvari_tp_files_no_dups.sh {params} {input}"
SnakeMake From line 49 of Rules/determine_sv_sets_min_callers.smk 
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shell:
        "bash ./Scripts/aggregate_truvari_tp_files_no_dups.sh {params} {input}"
SnakeMake From line 66 of Rules/determine_sv_sets_min_callers.smk 
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shell:
        "bash ./Scripts/aggregate_truvari_tp_files_no_dups.sh {params} {input}"
SnakeMake From line 83 of Rules/determine_sv_sets_min_callers.smk 
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shell:
        "bash ./Scripts/aggregate_truvari_tp_files_no_dups.sh {params} {input}"
SnakeMake From line 102 of Rules/determine_sv_sets_min_callers.smk 
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shell:
        "bash ./Scripts/aggregate_truvari_tp_files_no_dups.sh {params} {input}"
SnakeMake From line 121 of Rules/determine_sv_sets_min_callers.smk 
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shell:
        "bash ./Scripts/aggregate_truvari_tp_files_no_dups.sh {params} {input}"
SnakeMake From line 140 of Rules/determine_sv_sets_min_callers.smk 
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shell:
        "bash ./Scripts/aggregate_truvari_tp_files_no_dups.sh {params} {input}"
SnakeMake From line 159 of Rules/determine_sv_sets_min_callers.smk 
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shell:
        "bash ./Scripts/aggregate_truvari_tp_files_no_dups.sh {params} {input}"
SnakeMake From line 178 of Rules/determine_sv_sets_min_callers.smk 
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shell:
        "bash ./Scripts/aggregate_truvari_tp_files_no_dups.sh {params} {input}"
SnakeMake From line 195 of Rules/determine_sv_sets_min_callers.smk 
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shell:
        "bash ./Scripts/aggregate_truvari_tp_files_no_dups.sh {params} {input}"
SnakeMake From line 212 of Rules/determine_sv_sets_min_callers.smk 
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shell:
        "bash ./Scripts/aggregate_truvari_tp_files_no_dups.sh {params} {input}"
SnakeMake From line 229 of Rules/determine_sv_sets_min_callers.smk 
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shell:
        "bash ./Scripts/aggregate_truvari_tp_files_no_dups.sh {params} {input}"
SnakeMake From line 246 of Rules/determine_sv_sets_min_callers.smk 
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shell:
        "bash ./Scripts/aggregate_truvari_tp_files_no_dups.sh {params} {input}"
SnakeMake From line 263 of Rules/determine_sv_sets_min_callers.smk 
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shell:
        "mkdir -p {params.genomesDir};\n"
        "bash ./Scripts/filter_genome_fasta.sh {input} {params.seqNames} {output}"
SnakeMake From line 12 of Rules/filter_genomes.smk 
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shell:
        "mkdir -p {params.genomesDir};\n"
        "bash ./Scripts/filter_genome_fasta.sh {input} {params.seqNames} {output}"
SnakeMake From line 27 of Rules/filter_genomes.smk 
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shell:
        "bash ./Scripts/summarize_SV_counts.sh W DEL {output} {input.allVCFs} {input.ssmDEL} {input.smlDEL} {input.medDEL} {input.lrgDEL};\n"
        "bash ./Scripts/summarize_SV_counts.sh A INS {output} {input.allVCFs} {input.ssmINS} {input.smlINS} {input.medINS} {input.lrgINS};\n"
        "bash ./Scripts/summarize_SV_counts.sh A DUP {output} {input.allVCFs} {input.ssmDUP} {input.smlDUP} {input.medDUP} {input.lrgDUP};\n"
        "bash ./Scripts/summarize_SV_counts.sh A INV {output} {input.allVCFs} {input.ssmINV} {input.smlINV} {input.medINV} {input.lrgINV};\n"
        "bash ./Scripts/summarize_SV_counts.sh A BND {output} {input.allVCFs};\n"
        "bash ./Scripts/total_SV_counts.sh {output}"
SnakeMake From line 28 of Rules/generate_final_result_counts.smk 
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shell:
        "bash ./Scripts/summarize_SV_counts.sh W DEL {output} {input.allVCFs} {input.ssmDEL} {input.smlDEL} {input.medDEL} {input.lrgDEL};\n"
        "bash ./Scripts/summarize_SV_counts.sh A INS {output} {input.allVCFs} {input.ssmINS} {input.smlINS} {input.medINS} {input.lrgINS};\n"
        "bash ./Scripts/summarize_SV_counts.sh A DUP {output} {input.allVCFs} {input.ssmDUP} {input.smlDUP} {input.medDUP} {input.lrgDUP};\n"
        "bash ./Scripts/summarize_SV_counts.sh A INV {output} {input.allVCFs} {input.ssmINV} {input.smlINV} {input.medINV} {input.lrgINV};\n"
        "bash ./Scripts/summarize_SV_counts.sh A BND {output} {input.allVCFs};\n"
        "bash ./Scripts/total_SV_counts.sh {output}"
SnakeMake From line 63 of Rules/generate_final_result_counts.smk 
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shell:
        "bash ./Scripts/summarize_SV_counts.sh W DEL {output} {input.allVCFs} {input.ssmDEL} {input.smlDEL} {input.medDEL} {input.lrgDEL};\n"
        "bash ./Scripts/summarize_SV_counts.sh A INS {output} {input.allVCFs} {input.ssmINS} {input.smlINS} {input.medINS} {input.lrgINS};\n"
        "bash ./Scripts/summarize_SV_counts.sh A DUP {output} {input.allVCFs} {input.ssmDUP} {input.smlDUP} {input.medDUP} {input.lrgDUP};\n"
        "bash ./Scripts/summarize_SV_counts.sh A INV {output} {input.allVCFs} {input.ssmINV} {input.smlINV} {input.medINV} {input.lrgINV};\n"
        "bash ./Scripts/summarize_SV_counts.sh A BND {output} {input.allVCFs};\n"
        "bash ./Scripts/total_SV_counts.sh {output}"
SnakeMake From line 98 of Rules/generate_final_result_counts.smk 
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shell:
        "bash ./Scripts/summarize_SV_counts.sh W DEL {output} {input.allVCFs} {input.ssmDEL} {input.smlDEL} {input.medDEL} {input.lrgDEL};\n"
        "bash ./Scripts/summarize_SV_counts.sh A INS {output} {input.allVCFs} {input.ssmINS} {input.smlINS} {input.medINS} {input.lrgINS};\n"
        "bash ./Scripts/summarize_SV_counts.sh A DUP {output} {input.allVCFs} {input.ssmDUP} {input.smlDUP} {input.medDUP} {input.lrgDUP};\n"
        "bash ./Scripts/summarize_SV_counts.sh A INV {output} {input.allVCFs} {input.ssmINV} {input.smlINV} {input.medINV} {input.lrgINV};\n"
        "bash ./Scripts/summarize_SV_counts.sh A BND {output} {input.allVCFs};\n"
        "bash ./Scripts/total_SV_counts.sh {output}"
SnakeMake From line 133 of Rules/generate_final_result_counts.smk 
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shell:
        "bash ./Scripts/summarize_SV_counts.sh W DEL {output} {input.allVCFs} {input.ssmDEL} {input.smlDEL} {input.medDEL} {input.lrgDEL};\n"
        "bash ./Scripts/summarize_SV_counts.sh A INS {output} {input.allVCFs} {input.ssmINS} {input.smlINS} {input.medINS} {input.lrgINS};\n"
        "bash ./Scripts/summarize_SV_counts.sh A INV {output} {input.allVCFs} {input.ssmINV} {input.smlINV} {input.medINV} {input.lrgINV};\n"
        "bash ./Scripts/total_SV_counts.sh {output}"
SnakeMake From line 163 of Rules/generate_final_result_counts.smk 
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shell:
        "bash ./Scripts/total_intersection_with_pav_counts.sh {output} {input}"
SnakeMake From line 181 of Rules/generate_final_result_counts.smk 
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shell:
        "bash ./Scripts/total_intersection_no_pav_counts.sh {output} {input}"
SnakeMake From line 196 of Rules/generate_final_result_counts.smk 
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shell:
        "bash ./Scripts/total_intersection_no_pav_counts.sh {output} {input}"
SnakeMake From line 211 of Rules/generate_final_result_counts.smk 
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shell:
        "bash ./Scripts/total_intersection_no_pav_counts.sh {output} {input}"
SnakeMake From line 226 of Rules/generate_final_result_counts.smk 
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shell:
        "bash ./Scripts/total_intersection_with_pav_counts.sh {output} {input}"
SnakeMake From line 241 of Rules/generate_final_result_counts.smk 
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shell:
        "bash ./Scripts/total_intersection_with_pav_counts.sh {output} {input}"
SnakeMake From line 256 of Rules/generate_final_result_counts.smk 
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shell:
        "bash ./Scripts/total_intersection_with_pav_counts.sh {output} {input}"
SnakeMake From line 271 of Rules/generate_final_result_counts.smk 
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shell:
        "bash ./Scripts/total_intersection_no_pav_counts.sh {output} {input}"
SnakeMake From line 286 of Rules/generate_final_result_counts.smk 
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shell:
        "bash ./Scripts/total_intersection_no_pav_counts.sh {output} {input}"
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        "bash ./Scripts/total_intersection_with_pav_counts.sh {output} {input}"
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        "bash ./Scripts/total_intersection_with_pav_counts.sh {output} {input}"
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        "bash ./Scripts/total_intersection_with_pav_counts.sh {output} {input}"
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        "bash ./Scripts/total_intersection_no_pav_counts.sh {output} {input}"
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        "bash ./Scripts/total_intersection_no_pav_counts.sh {output} {input}"
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        "bash ./Scripts/total_intersection_no_pav_counts.sh {output} {input}"
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        "bash ./Scripts/total_intersection_with_pav_counts.sh {output} {input}"
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        "bash ./Scripts/total_intersection_with_pav_counts.sh {output} {input}"
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        "bash ./Scripts/total_intersection_with_pav_counts.sh {output} {input}"
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        "bash ./Scripts/total_intersection_no_pav_counts.sh {output} {input}"
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        "bash ./Scripts/total_intersection_with_pav_counts.sh {output} {input}"
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        "bash ./Scripts/total_intersection_with_pav_counts.sh {output} {input}"
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        "bash ./Scripts/total_intersection_no_pav_counts.sh {output} {input}"
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        "bash ./Scripts/total_intersection_with_pav_counts.sh {output} {input}"
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shell:
        "mkdir -p {params.svOutDir};\n"
        "cuteSV --min_size {params.minSize} --max_size {params.maxSize} -s {params.minSupp} --max_cluster_bias_INS {params.clusterBias} "
        "--diff_ratio_merging_INS {params.diffRatio} --max_cluster_bias_DEL {params.clusterBias} --diff_ratio_merging_DEL {params.diffRatio} {input.inputFile} "
        "{params.refGenome} {output} {params.svOutDir}"
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shell:
        "mkdir -p {params.svOutDir};\n"
        "sniffles --threads {threads} --mapq {params.minMAPQ} --minsupport {params.minSupp} --minsvlen {params.minSize} "
        "--reference {params.refGenome} -i {input.inputFile} -v {output}"
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shell:
        "mkdir -p {params.svOutDir};\n"
        "svim alignment --min_sv_size {params.minSize} --max_sv_size {params.maxSize} --min_mapq {params.minMAPQ}  {params.svOutDir} {input.inputFile} {params.refGenome};"
        "mv {params.svOutDir}/variants.vcf {params.svOutDir}/{params.refName}.svim.ALL.unfiltered.vcf"
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        "bash Scripts/prefetch_read_files_list.sh {params.readsOutDir} {params.maxFileSize} {input}"
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        "bash ./Scripts/fasterq_dump_read_files.sh {threads} {params.readsOutDir} {input.readFilesList} {params.maxFileSize}"
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        "uniq {input.minTwo} > {output.uniqueTwo};\n"
        "uniq {input.minThree} > {output.uniqueThree};\n"
        "uniq {input.minFour} > {output.uniqueFour}"
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shell:
        "uniq {input.minTwo} > {output.uniqueTwo};\n"
        "uniq {input.minThree} > {output.uniqueThree};\n"
        "uniq {input.minFour} > {output.uniqueFour}"
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        "uniq {input.minTwo} > {output.uniqueTwo};\n"
        "uniq {input.minThree} > {output.uniqueThree};\n"
        "uniq {input.minFour} > {output.uniqueFour}"
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shell:
        "uniq {input.minTwo} > {output.uniqueTwo};\n"
        "uniq {input.minThree} > {output.uniqueThree};\n"
        "uniq {input.minFour} > {output.uniqueFour}"
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        "uniq {input.minTwo} > {output.uniqueTwo};\n"
        "uniq {input.minThree} > {output.uniqueThree};\n"
        "uniq {input.minFour} > {output.uniqueFour}"
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        "bash ./Scripts/segment_sv_types_w_bcftools.sh {input} {params}"
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        "bash ./Scripts/segment_sv_types_w_bcftools.sh {input} {params}"
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        "bash ./Scripts/segment_sv_types_w_bcftools.sh {input} {params}"
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        "bash ./Scripts/segment_sv_types_w_bcftools.sh {input} {params}"
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        "bash ./Scripts/segment_pav_w_bcftools.sh {input} {params}"
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        "samtools sort -m{params} -@ {threads} -o {output} {input}"
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        "samtools index -@ {threads} {input}"
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        "samtools sort -m{params} -@ {threads} -o {output} {input}"
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        "samtools index -@ {threads} {input}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DEL {output} W {input.summaryDELSSm} {input.summaryDELSml} {input.summaryDELMed} {input.summaryDELLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INS {output} A {input.summaryINSSSm} {input.summaryINSSml} {input.summaryINSMed} {input.summaryINSLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DUP {output} A {input.summaryDUPSSm} {input.summaryDUPSml} {input.summaryDUPMed} {input.summaryDUPLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INV {output} A {input.summaryINVSSm} {input.summaryINVSml} {input.summaryINVMed} {input.summaryINVLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} BND {output} A {input.summaryBND};\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DEL {output} W {input.summaryDELSSm} {input.summaryDELSml} {input.summaryDELMed} {input.summaryDELLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INS {output} A {input.summaryINSSSm} {input.summaryINSSml} {input.summaryINSMed} {input.summaryINSLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DUP {output} A {input.summaryDUPSSm} {input.summaryDUPSml} {input.summaryDUPMed} {input.summaryDUPLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INV {output} A {input.summaryINVSSm} {input.summaryINVSml} {input.summaryINVMed} {input.summaryINVLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} BND {output} A {input.summaryBND};\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DEL {output} W {input.summaryDELSSm} {input.summaryDELSml} {input.summaryDELMed} {input.summaryDELLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INS {output} A {input.summaryINSSSm} {input.summaryINSSml} {input.summaryINSMed} {input.summaryINSLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DUP {output} A {input.summaryDUPSSm} {input.summaryDUPSml} {input.summaryDUPMed} {input.summaryDUPLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INV {output} A {input.summaryINVSSm} {input.summaryINVSml} {input.summaryINVMed} {input.summaryINVLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} BND {output} A {input.summaryBND};\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DEL {output} W {input.summaryDELSSm} {input.summaryDELSml} {input.summaryDELMed} {input.summaryDELLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INS {output} A {input.summaryINSSSm} {input.summaryINSSml} {input.summaryINSMed} {input.summaryINSLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DUP {output} A {input.summaryDUPSSm} {input.summaryDUPSml} {input.summaryDUPMed} {input.summaryDUPLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INV {output} A {input.summaryINVSSm} {input.summaryINVSml} {input.summaryINVMed} {input.summaryINVLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} BND {output} A {input.summaryBND};\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DEL {output} W {input.summaryDELSSm} {input.summaryDELSml} {input.summaryDELMed} {input.summaryDELLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INS {output} A {input.summaryINSSSm} {input.summaryINSSml} {input.summaryINSMed} {input.summaryINSLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DUP {output} A {input.summaryDUPSSm} {input.summaryDUPSml} {input.summaryDUPMed} {input.summaryDUPLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INV {output} A {input.summaryINVSSm} {input.summaryINVSml} {input.summaryINVMed} {input.summaryINVLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} BND {output} A {input.summaryBND};\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DEL {output} W {input.summaryDELSSm} {input.summaryDELSml} {input.summaryDELMed} {input.summaryDELLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INS {output} A {input.summaryINSSSm} {input.summaryINSSml} {input.summaryINSMed} {input.summaryINSLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DUP {output} A {input.summaryDUPSSm} {input.summaryDUPSml} {input.summaryDUPMed} {input.summaryDUPLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INV {output} A {input.summaryINVSSm} {input.summaryINVSml} {input.summaryINVMed} {input.summaryINVLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} BND {output} A {input.summaryBND};\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DEL {output} W {input.summaryDELSSm} {input.summaryDELSml} {input.summaryDELMed} {input.summaryDELLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INS {output} A {input.summaryINSSSm} {input.summaryINSSml} {input.summaryINSMed} {input.summaryINSLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INV {output} A {input.summaryINVSSm} {input.summaryINVSml} {input.summaryINVMed} {input.summaryINVLrg};\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DEL {output} W {input.summaryDELSSm} {input.summaryDELSml} {input.summaryDELMed} {input.summaryDELLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INS {output} A {input.summaryINSSSm} {input.summaryINSSml} {input.summaryINSMed} {input.summaryINSLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INV {output} A {input.summaryINVSSm} {input.summaryINVSml} {input.summaryINVMed} {input.summaryINVLrg};\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DEL {output} W {input.summaryDELSSm} {input.summaryDELSml} {input.summaryDELMed} {input.summaryDELLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INS {output} A {input.summaryINSSSm} {input.summaryINSSml} {input.summaryINSMed} {input.summaryINSLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INV {output} A {input.summaryINVSSm} {input.summaryINVSml} {input.summaryINVMed} {input.summaryINVLrg};\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DEL {output} W {input.summaryDELSSm} {input.summaryDELSml} {input.summaryDELMed} {input.summaryDELLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INS {output} A {input.summaryINSSSm} {input.summaryINSSml} {input.summaryINSMed} {input.summaryINSLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INV {output} A {input.summaryINVSSm} {input.summaryINVSml} {input.summaryINVMed} {input.summaryINVLrg};\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DEL {output} W {input.summaryDELSSm} {input.summaryDELSml} {input.summaryDELMed} {input.summaryDELLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INS {output} A {input.summaryINSSSm} {input.summaryINSSml} {input.summaryINSMed} {input.summaryINSLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DUP {output} A {input.summaryDUPSSm} {input.summaryDUPSml} {input.summaryDUPMed} {input.summaryDUPLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INV {output} A {input.summaryINVSSm} {input.summaryINVSml} {input.summaryINVMed} {input.summaryINVLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} BND {output} A {input.summaryBND};\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DEL {output} W {input.summaryDELSSm} {input.summaryDELSml} {input.summaryDELMed} {input.summaryDELLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INS {output} A {input.summaryINSSSm} {input.summaryINSSml} {input.summaryINSMed} {input.summaryINSLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INV {output} A {input.summaryINVSSm} {input.summaryINVSml} {input.summaryINVMed} {input.summaryINVLrg};\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DEL {output} W {input.summaryDELSSm} {input.summaryDELSml} {input.summaryDELMed} {input.summaryDELLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INS {output} A {input.summaryINSSSm} {input.summaryINSSml} {input.summaryINSMed} {input.summaryINSLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INV {output} A {input.summaryINVSSm} {input.summaryINVSml} {input.summaryINVMed} {input.summaryINVLrg};\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DEL {output} W {input.summaryDELSSm} {input.summaryDELSml} {input.summaryDELMed} {input.summaryDELLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INS {output} A {input.summaryINSSSm} {input.summaryINSSml} {input.summaryINSMed} {input.summaryINSLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INV {output} A {input.summaryINVSSm} {input.summaryINVSml} {input.summaryINVMed} {input.summaryINVLrg};\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DEL {output} W {input.summaryDELSSm} {input.summaryDELSml} {input.summaryDELMed} {input.summaryDELLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INS {output} A {input.summaryINSSSm} {input.summaryINSSml} {input.summaryINSMed} {input.summaryINSLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INV {output} A {input.summaryINVSSm} {input.summaryINVSml} {input.summaryINVMed} {input.summaryINVLrg};\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 508 of Rules/summarize_tool_evaluation_rates_all.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DEL {output} W {input.summaryDELSSm} {input.summaryDELSml} {input.summaryDELMed} {input.summaryDELLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INS {output} A {input.summaryINSSSm} {input.summaryINSSml} {input.summaryINSMed} {input.summaryINSLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INV {output} A {input.summaryINVSSm} {input.summaryINVSml} {input.summaryINVMed} {input.summaryINVLrg};\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 538 of Rules/summarize_tool_evaluation_rates_all.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DEL {output} W {input.summaryDELSSm} {input.summaryDELSml} {input.summaryDELMed} {input.summaryDELLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INS {output} A {input.summaryINSSSm} {input.summaryINSSml} {input.summaryINSMed} {input.summaryINSLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INV {output} A {input.summaryINVSSm} {input.summaryINVSml} {input.summaryINVMed} {input.summaryINVLrg};\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 568 of Rules/summarize_tool_evaluation_rates_all.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DEL {output} W {input.summaryDELSSm} {input.summaryDELSml} {input.summaryDELMed} {input.summaryDELLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INS {output} A {input.summaryINSSSm} {input.summaryINSSml} {input.summaryINSMed} {input.summaryINSLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DUP {output} A {input.summaryDUPSSm} {input.summaryDUPSml} {input.summaryDUPMed} {input.summaryDUPLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INV {output} A {input.summaryINVSSm} {input.summaryINVSml} {input.summaryINVMed} {input.summaryINVLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} BND {output} A {input.summaryBND};\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 605 of Rules/summarize_tool_evaluation_rates_all.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DEL {output} W {input.summaryDELSSm} {input.summaryDELSml} {input.summaryDELMed} {input.summaryDELLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INS {output} A {input.summaryINSSSm} {input.summaryINSSml} {input.summaryINSMed} {input.summaryINSLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DUP {output} A {input.summaryDUPSSm} {input.summaryDUPSml} {input.summaryDUPMed} {input.summaryDUPLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INV {output} A {input.summaryINVSSm} {input.summaryINVSml} {input.summaryINVMed} {input.summaryINVLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} BND {output} A {input.summaryBND};\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DEL {output} W {input.summaryDELSSm} {input.summaryDELSml} {input.summaryDELMed} {input.summaryDELLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INS {output} A {input.summaryINSSSm} {input.summaryINSSml} {input.summaryINSMed} {input.summaryINSLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DUP {output} A {input.summaryDUPSSm} {input.summaryDUPSml} {input.summaryDUPMed} {input.summaryDUPLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INV {output} A {input.summaryINVSSm} {input.summaryINVSml} {input.summaryINVMed} {input.summaryINVLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} BND {output} A {input.summaryBND};\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 683 of Rules/summarize_tool_evaluation_rates_all.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DEL {output} W {input.summaryDELSSm} {input.summaryDELSml} {input.summaryDELMed} {input.summaryDELLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INS {output} A {input.summaryINSSSm} {input.summaryINSSml} {input.summaryINSMed} {input.summaryINSLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DUP {output} A {input.summaryDUPSSm} {input.summaryDUPSml} {input.summaryDUPMed} {input.summaryDUPLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INV {output} A {input.summaryINVSSm} {input.summaryINVSml} {input.summaryINVMed} {input.summaryINVLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} BND {output} A {input.summaryBND};\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 722 of Rules/summarize_tool_evaluation_rates_all.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DEL {output} W {input.summaryDELSSm} {input.summaryDELSml} {input.summaryDELMed} {input.summaryDELLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INS {output} A {input.summaryINSSSm} {input.summaryINSSml} {input.summaryINSMed} {input.summaryINSLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INV {output} A {input.summaryINVSSm} {input.summaryINVSml} {input.summaryINVMed} {input.summaryINVLrg};\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 754 of Rules/summarize_tool_evaluation_rates_all.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DEL {output} W {input.summaryDELSSm} {input.summaryDELSml} {input.summaryDELMed} {input.summaryDELLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INS {output} A {input.summaryINSSSm} {input.summaryINSSml} {input.summaryINSMed} {input.summaryINSLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INV {output} A {input.summaryINVSSm} {input.summaryINVSml} {input.summaryINVMed} {input.summaryINVLrg};\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 784 of Rules/summarize_tool_evaluation_rates_all.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DEL {output} W {input.summaryDELSSm} {input.summaryDELSml} {input.summaryDELMed} {input.summaryDELLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INS {output} A {input.summaryINSSSm} {input.summaryINSSml} {input.summaryINSMed} {input.summaryINSLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INV {output} A {input.summaryINVSSm} {input.summaryINVSml} {input.summaryINVMed} {input.summaryINVLrg};\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 814 of Rules/summarize_tool_evaluation_rates_all.smk 
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        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DEL {output} W {input.summaryDELSSm} {input.summaryDELSml} {input.summaryDELMed} {input.summaryDELLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INS {output} A {input.summaryINSSSm} {input.summaryINSSml} {input.summaryINSMed} {input.summaryINSLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INV {output} A {input.summaryINVSSm} {input.summaryINVSml} {input.summaryINVMed} {input.summaryINVLrg};\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} DEL {output} W {input.summaryDELSSm} {input.summaryDELSml} {input.summaryDELMed} {input.summaryDELLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INS {output} A {input.summaryINSSSm} {input.summaryINSSml} {input.summaryINSMed} {input.summaryINSLrg};\n"
        "bash ./Scripts/calculate_iou_from_truvari_list.sh {params.toolA} {params.toolB} INV {output} A {input.summaryINVSSm} {input.summaryINVSml} {input.summaryINVMed} {input.summaryINVLrg};\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 874 of Rules/summarize_tool_evaluation_rates_all.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 15 of Rules/summarize_tool_evaluation_rates_lrg.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 36 of Rules/summarize_tool_evaluation_rates_lrg.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 78 of Rules/summarize_tool_evaluation_rates_lrg.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
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        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} BND {input.summaryBND} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 16 of Rules/summarize_tool_evaluation_rates_ssm.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} BND {input.summaryBND} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 39 of Rules/summarize_tool_evaluation_rates_ssm.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} BND {input.summaryBND} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 62 of Rules/summarize_tool_evaluation_rates_ssm.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} BND {input.summaryBND} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 85 of Rules/summarize_tool_evaluation_rates_ssm.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} BND {input.summaryBND} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 108 of Rules/summarize_tool_evaluation_rates_ssm.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} BND {input.summaryBND} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 131 of Rules/summarize_tool_evaluation_rates_ssm.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 152 of Rules/summarize_tool_evaluation_rates_ssm.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 171 of Rules/summarize_tool_evaluation_rates_ssm.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 190 of Rules/summarize_tool_evaluation_rates_ssm.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 209 of Rules/summarize_tool_evaluation_rates_ssm.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} BND {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 230 of Rules/summarize_tool_evaluation_rates_ssm.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 251 of Rules/summarize_tool_evaluation_rates_ssm.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 270 of Rules/summarize_tool_evaluation_rates_ssm.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 289 of Rules/summarize_tool_evaluation_rates_ssm.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 308 of Rules/summarize_tool_evaluation_rates_ssm.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 327 of Rules/summarize_tool_evaluation_rates_ssm.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 346 of Rules/summarize_tool_evaluation_rates_ssm.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} BND {input.summaryBND} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 367 of Rules/summarize_tool_evaluation_rates_ssm.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} BND {input.summaryBND} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 390 of Rules/summarize_tool_evaluation_rates_ssm.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} BND {input.summaryBND} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 413 of Rules/summarize_tool_evaluation_rates_ssm.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DUP {input.summaryDUP} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} BND {input.summaryBND} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 436 of Rules/summarize_tool_evaluation_rates_ssm.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 457 of Rules/summarize_tool_evaluation_rates_ssm.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 476 of Rules/summarize_tool_evaluation_rates_ssm.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 495 of Rules/summarize_tool_evaluation_rates_ssm.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 514 of Rules/summarize_tool_evaluation_rates_ssm.smk 
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shell:
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} DEL {input.summaryDEL} {output} W;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INS {input.summaryINS} {output} A;\n"
        "bash ./Scripts/calculate_iou_from_truvari_pair.sh {params.toolA} {params.toolB} INV {input.summaryINV} {output} A;\n"
        "bash ./Scripts/calculate_total_from_tsv.sh {output} {params.toolA} {params.toolB}"
SnakeMake From line 536 of Rules/summarize_tool_evaluation_rates_ssm.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.snifflesDEL} {input.svimDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.snifflesINS} {input.svimINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_pairs.sh {input.snifflesDUP} {input.svimDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.snifflesINV} {input.svimINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Lrg;\n"
SnakeMake From line 35 of Rules/truvari_bench_sv_files_lrg.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.cuteSVDEL} {input.snifflesDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.cuteSVINS} {input.snifflesINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_pairs.sh {input.cuteSVDUP} {input.snifflesDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.cuteSVINV} {input.snifflesINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Lrg;\n"
SnakeMake From line 75 of Rules/truvari_bench_sv_files_lrg.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.cuteSVDEL} {input.svimDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.cuteSVINS} {input.svimINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_pairs.sh {input.cuteSVDUP} {input.svimDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.cuteSVINV} {input.svimINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Lrg;\n"
SnakeMake From line 111 of Rules/truvari_bench_sv_files_lrg.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.cuteSVDEL} {input.svimASMDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.cuteSVINS} {input.svimASMINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_pairs.sh {input.cuteSVDUP} {input.svimASMDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/Lrg;\n"
        "bash ./Scripts/compare_breakends_w_truvari_pairs.sh {input.cuteSVINV} {input.svimASMINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Lrg;\n"
SnakeMake From line 151 of Rules/truvari_bench_sv_files_lrg.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.snifflesDEL} {input.svimASMDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.snifflesINS} {input.svimASMINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_pairs.sh {input.snifflesDUP} {input.svimASMDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/Lrg;\n"
        "bash ./Scripts/compare_breakends_w_truvari_pairs.sh {input.snifflesINV} {input.svimASMINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Lrg;\n"
SnakeMake From line 191 of Rules/truvari_bench_sv_files_lrg.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.svimDEL} {input.svimASMDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.svimINS} {input.svimASMINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_pairs.sh {input.svimDUP} {input.svimASMDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/Lrg;\n"
        "bash ./Scripts/compare_breakends_w_truvari_pairs.sh {input.svimINV} {input.svimASMINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Lrg;\n"
SnakeMake From line 231 of Rules/truvari_bench_sv_files_lrg.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.cuteSVDEL} {input.pavDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.cuteSVINS} {input.pavINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.cuteSVINV} {input.pavINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Lrg"
SnakeMake From line 266 of Rules/truvari_bench_sv_files_lrg.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.pavDEL} {input.snifflesDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.pavINS} {input.snifflesINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.pavINV} {input.snifflesINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Lrg"
SnakeMake From line 300 of Rules/truvari_bench_sv_files_lrg.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.pavDEL} {input.svimDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.pavINS} {input.svimINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.pavINV} {input.svimINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Lrg"
SnakeMake From line 334 of Rules/truvari_bench_sv_files_lrg.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.pavDEL} {input.svimASMDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.pavINS} {input.svimASMINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Lrg;\n"
        "bash ./Scripts/compare_breakends_w_truvari_pairs.sh {input.pavINV} {input.svimASMINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Lrg"
SnakeMake From line 368 of Rules/truvari_bench_sv_files_lrg.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_trips.sh {input.setOneDUP} {params.setTwoDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/Lrg;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Lrg;\n"
SnakeMake From line 427 of Rules/truvari_bench_sv_files_lrg.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Lrg;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Lrg"
SnakeMake From line 477 of Rules/truvari_bench_sv_files_lrg.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Lrg;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Lrg"
SnakeMake From line 526 of Rules/truvari_bench_sv_files_lrg.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Lrg;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Lrg"
SnakeMake From line 575 of Rules/truvari_bench_sv_files_lrg.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Lrg"
SnakeMake From line 624 of Rules/truvari_bench_sv_files_lrg.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Lrg;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Lrg"
SnakeMake From line 673 of Rules/truvari_bench_sv_files_lrg.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Lrg;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Lrg"
SnakeMake From line 722 of Rules/truvari_bench_sv_files_lrg.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_trips.sh {input.setOneDUP} {params.setTwoDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/Lrg;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Lrg;\n"
SnakeMake From line 781 of Rules/truvari_bench_sv_files_lrg.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_trips.sh {input.setOneDUP} {params.setTwoDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/Lrg;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Lrg;\n"
SnakeMake From line 841 of Rules/truvari_bench_sv_files_lrg.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_trips.sh {input.setOneDUP} {params.setTwoDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/Lrg;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Lrg;\n"
SnakeMake From line 901 of Rules/truvari_bench_sv_files_lrg.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_quads.sh {params.setOneDUP} {params.setTwoDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/Lrg;\n"
        "bash ./Scripts/compare_breakends_w_truvari_quads.sh {params.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Lrg;\n"
SnakeMake From line 981 of Rules/truvari_bench_sv_files_lrg.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Lrg;\n"
        "bash ./Scripts/compare_breakends_w_truvari_quads.sh {params.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Lrg"
SnakeMake From line 1046 of Rules/truvari_bench_sv_files_lrg.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Lrg;\n"
        "bash ./Scripts/compare_breakends_w_truvari_quads.sh {params.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Lrg"
SnakeMake From line 1110 of Rules/truvari_bench_sv_files_lrg.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Lrg;\n"
        "bash ./Scripts/compare_breakends_w_truvari_quads.sh {params.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Lrg"
SnakeMake From line 1174 of Rules/truvari_bench_sv_files_lrg.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Lrg;\n"
        "bash ./Scripts/compare_breakends_w_truvari_quads.sh {params.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Lrg"
SnakeMake From line 1238 of Rules/truvari_bench_sv_files_lrg.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_all.sh {params.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Lrg;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_all.sh {params.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Lrg;\n"
        "bash ./Scripts/compare_breakends_w_truvari_all.sh {params.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Lrg"
SnakeMake From line 1319 of Rules/truvari_bench_sv_files_lrg.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.snifflesDEL} {input.svimDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.snifflesINS} {input.svimINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_pairs.sh {input.snifflesDUP} {input.svimDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.snifflesINV} {input.svimINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Med;\n"
SnakeMake From line 35 of Rules/truvari_bench_sv_files_med.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.cuteSVDEL} {input.snifflesDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.cuteSVINS} {input.snifflesINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_pairs.sh {input.cuteSVDUP} {input.snifflesDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.cuteSVINV} {input.snifflesINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Med;\n"
SnakeMake From line 75 of Rules/truvari_bench_sv_files_med.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.cuteSVDEL} {input.svimDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.cuteSVINS} {input.svimINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_pairs.sh {input.cuteSVDUP} {input.svimDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.cuteSVINV} {input.svimINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Med;\n"
SnakeMake From line 111 of Rules/truvari_bench_sv_files_med.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.cuteSVDEL} {input.svimASMDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.cuteSVINS} {input.svimASMINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_pairs.sh {input.cuteSVDUP} {input.svimASMDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/Med;\n"
        "bash ./Scripts/compare_breakends_w_truvari_pairs.sh {input.cuteSVINV} {input.svimASMINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Med;\n"
SnakeMake From line 151 of Rules/truvari_bench_sv_files_med.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.snifflesDEL} {input.svimASMDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.snifflesINS} {input.svimASMINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_pairs.sh {input.snifflesDUP} {input.svimASMDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/Med;\n"
        "bash ./Scripts/compare_breakends_w_truvari_pairs.sh {input.snifflesINV} {input.svimASMINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Med;\n"
SnakeMake From line 191 of Rules/truvari_bench_sv_files_med.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.svimDEL} {input.svimASMDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.svimINS} {input.svimASMINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_pairs.sh {input.svimDUP} {input.svimASMDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/Med;\n"
        "bash ./Scripts/compare_breakends_w_truvari_pairs.sh {input.svimINV} {input.svimASMINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Med;\n"
SnakeMake From line 231 of Rules/truvari_bench_sv_files_med.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.cuteSVDEL} {input.pavDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.cuteSVINS} {input.pavINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.cuteSVINV} {input.pavINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Med"
SnakeMake From line 266 of Rules/truvari_bench_sv_files_med.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.pavDEL} {input.snifflesDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.pavINS} {input.snifflesINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.pavINV} {input.snifflesINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Med"
SnakeMake From line 300 of Rules/truvari_bench_sv_files_med.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.pavDEL} {input.svimDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.pavINS} {input.svimINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.pavINV} {input.svimINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Med"
SnakeMake From line 334 of Rules/truvari_bench_sv_files_med.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.pavDEL} {input.svimASMDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.pavINS} {input.svimASMINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Med;\n"
        "bash ./Scripts/compare_breakends_w_truvari_pairs.sh {input.pavINV} {input.svimASMINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Med"
SnakeMake From line 368 of Rules/truvari_bench_sv_files_med.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_trips.sh {input.setOneDUP} {params.setTwoDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/Med;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Med;\n"
SnakeMake From line 427 of Rules/truvari_bench_sv_files_med.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Med;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Med"
SnakeMake From line 477 of Rules/truvari_bench_sv_files_med.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Med;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Med"
SnakeMake From line 526 of Rules/truvari_bench_sv_files_med.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Med;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Med"
SnakeMake From line 575 of Rules/truvari_bench_sv_files_med.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Med"
SnakeMake From line 624 of Rules/truvari_bench_sv_files_med.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Med;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Med"
SnakeMake From line 673 of Rules/truvari_bench_sv_files_med.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Med;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Med"
SnakeMake From line 722 of Rules/truvari_bench_sv_files_med.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_trips.sh {input.setOneDUP} {params.setTwoDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/Med;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Med;\n"
SnakeMake From line 781 of Rules/truvari_bench_sv_files_med.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_trips.sh {input.setOneDUP} {params.setTwoDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/Med;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Med;\n"
SnakeMake From line 841 of Rules/truvari_bench_sv_files_med.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_trips.sh {input.setOneDUP} {params.setTwoDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/Med;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Med;\n"
SnakeMake From line 901 of Rules/truvari_bench_sv_files_med.smk 
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        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_quads.sh {params.setOneDUP} {params.setTwoDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/Med;\n"
        "bash ./Scripts/compare_breakends_w_truvari_quads.sh {params.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Med;\n"
SnakeMake From line 981 of Rules/truvari_bench_sv_files_med.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Med;\n"
        "bash ./Scripts/compare_breakends_w_truvari_quads.sh {params.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Med"
SnakeMake From line 1046 of Rules/truvari_bench_sv_files_med.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Med;\n"
        "bash ./Scripts/compare_breakends_w_truvari_quads.sh {params.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Med"
SnakeMake From line 1110 of Rules/truvari_bench_sv_files_med.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Med;\n"
        "bash ./Scripts/compare_breakends_w_truvari_quads.sh {params.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Med"
SnakeMake From line 1174 of Rules/truvari_bench_sv_files_med.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Med;\n"
        "bash ./Scripts/compare_breakends_w_truvari_quads.sh {params.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Med"
SnakeMake From line 1238 of Rules/truvari_bench_sv_files_med.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_all.sh {params.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Med;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_all.sh {params.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Med;\n"
        "bash ./Scripts/compare_breakends_w_truvari_all.sh {params.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Med"
SnakeMake From line 1319 of Rules/truvari_bench_sv_files_med.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.snifflesDEL} {input.svimDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.snifflesINS} {input.svimINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_pairs.sh {input.snifflesDUP} {input.svimDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.snifflesINV} {input.svimINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Sml;\n"
SnakeMake From line 35 of Rules/truvari_bench_sv_files_sml.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.cuteSVDEL} {input.snifflesDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.cuteSVINS} {input.snifflesINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_pairs.sh {input.cuteSVDUP} {input.snifflesDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.cuteSVINV} {input.snifflesINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Sml;\n"
SnakeMake From line 75 of Rules/truvari_bench_sv_files_sml.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.cuteSVDEL} {input.svimDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.cuteSVINS} {input.svimINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_pairs.sh {input.cuteSVDUP} {input.svimDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.cuteSVINV} {input.svimINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Sml;\n"
SnakeMake From line 111 of Rules/truvari_bench_sv_files_sml.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.cuteSVDEL} {input.svimASMDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.cuteSVINS} {input.svimASMINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_pairs.sh {input.cuteSVDUP} {input.svimASMDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/Sml;\n"
        "bash ./Scripts/compare_breakends_w_truvari_pairs.sh {input.cuteSVINV} {input.svimASMINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Sml;\n"
SnakeMake From line 151 of Rules/truvari_bench_sv_files_sml.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.snifflesDEL} {input.svimASMDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.snifflesINS} {input.svimASMINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_pairs.sh {input.snifflesDUP} {input.svimASMDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/Sml;\n"
        "bash ./Scripts/compare_breakends_w_truvari_pairs.sh {input.snifflesINV} {input.svimASMINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Sml;\n"
SnakeMake From line 191 of Rules/truvari_bench_sv_files_sml.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.svimDEL} {input.svimASMDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.svimINS} {input.svimASMINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_pairs.sh {input.svimDUP} {input.svimASMDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/Sml;\n"
        "bash ./Scripts/compare_breakends_w_truvari_pairs.sh {input.svimINV} {input.svimASMINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Sml;\n"
SnakeMake From line 231 of Rules/truvari_bench_sv_files_sml.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.cuteSVDEL} {input.pavDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.cuteSVINS} {input.pavINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.cuteSVINV} {input.pavINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Sml"
SnakeMake From line 266 of Rules/truvari_bench_sv_files_sml.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.pavDEL} {input.snifflesDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.pavINS} {input.snifflesINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.pavINV} {input.snifflesINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Sml"
SnakeMake From line 300 of Rules/truvari_bench_sv_files_sml.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.pavDEL} {input.svimDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.pavINS} {input.svimINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.pavINV} {input.svimINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Sml"
SnakeMake From line 334 of Rules/truvari_bench_sv_files_sml.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.pavDEL} {input.svimASMDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_pairs.sh {input.pavINS} {input.svimASMINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Sml;\n"
        "bash ./Scripts/compare_breakends_w_truvari_pairs.sh {input.pavINV} {input.svimASMINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Sml"
SnakeMake From line 368 of Rules/truvari_bench_sv_files_sml.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_trips.sh {input.setOneDUP} {params.setTwoDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/Sml;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Sml;\n"
SnakeMake From line 427 of Rules/truvari_bench_sv_files_sml.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Sml;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Sml"
SnakeMake From line 477 of Rules/truvari_bench_sv_files_sml.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Sml;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Sml"
SnakeMake From line 526 of Rules/truvari_bench_sv_files_sml.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Sml;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Sml"
SnakeMake From line 575 of Rules/truvari_bench_sv_files_sml.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Sml"
SnakeMake From line 624 of Rules/truvari_bench_sv_files_sml.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Sml;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Sml"
SnakeMake From line 673 of Rules/truvari_bench_sv_files_sml.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Sml;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Sml"
SnakeMake From line 722 of Rules/truvari_bench_sv_files_sml.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_trips.sh {input.setOneDUP} {params.setTwoDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/Sml;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Sml;\n"
SnakeMake From line 781 of Rules/truvari_bench_sv_files_sml.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_trips.sh {input.setOneDUP} {params.setTwoDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/Sml;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Sml;\n"
SnakeMake From line 841 of Rules/truvari_bench_sv_files_sml.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_trips.sh {input.setOneDUP} {params.setTwoDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/Sml;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Sml;\n"
SnakeMake From line 901 of Rules/truvari_bench_sv_files_sml.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_quads.sh {params.setOneDUP} {params.setTwoDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/Sml;\n"
        "bash ./Scripts/compare_breakends_w_truvari_quads.sh {params.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Sml;\n"
SnakeMake From line 981 of Rules/truvari_bench_sv_files_sml.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Sml;\n"
        "bash ./Scripts/compare_breakends_w_truvari_quads.sh {params.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Sml"
SnakeMake From line 1046 of Rules/truvari_bench_sv_files_sml.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Sml;\n"
        "bash ./Scripts/compare_breakends_w_truvari_quads.sh {params.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Sml"
SnakeMake From line 1110 of Rules/truvari_bench_sv_files_sml.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Sml;\n"
        "bash ./Scripts/compare_breakends_w_truvari_quads.sh {params.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Sml"
SnakeMake From line 1174 of Rules/truvari_bench_sv_files_sml.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Sml;\n"
        "bash ./Scripts/compare_breakends_w_truvari_quads.sh {params.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Sml"
SnakeMake From line 1238 of Rules/truvari_bench_sv_files_sml.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_all.sh {params.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/Sml;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_all.sh {params.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/Sml;\n"
        "bash ./Scripts/compare_breakends_w_truvari_all.sh {params.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/Sml"
SnakeMake From line 1319 of Rules/truvari_bench_sv_files_sml.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/SSm;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/SSm;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_trips.sh {input.setOneDUP} {params.setTwoDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/SSm;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/SSm;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneBND} {params.setTwoBND} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/BND"
SnakeMake From line 492 of Rules/truvari_bench_sv_files_ssm.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/SSm;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/SSm;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/SSm"
SnakeMake From line 543 of Rules/truvari_bench_sv_files_ssm.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/SSm;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/SSm;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/SSm"
SnakeMake From line 592 of Rules/truvari_bench_sv_files_ssm.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/SSm;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/SSm;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/SSm"
SnakeMake From line 641 of Rules/truvari_bench_sv_files_ssm.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/SSm;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/SSm;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/SSm"
SnakeMake From line 690 of Rules/truvari_bench_sv_files_ssm.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/SSm;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/SSm;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/SSm"
SnakeMake From line 739 of Rules/truvari_bench_sv_files_ssm.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/SSm;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/SSm;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/SSm"
SnakeMake From line 788 of Rules/truvari_bench_sv_files_ssm.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/SSm;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/SSm;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_trips.sh {input.setOneDUP} {params.setTwoDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/SSm;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/SSm;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneBND} {params.setTwoBND} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/BND"
SnakeMake From line 857 of Rules/truvari_bench_sv_files_ssm.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/SSm;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/SSm;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_trips.sh {input.setOneDUP} {params.setTwoDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/SSm;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/SSm;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneBND} {params.setTwoBND} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/BND"
SnakeMake From line 928 of Rules/truvari_bench_sv_files_ssm.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/SSm;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_trips.sh {input.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/SSm;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_ignore_type_trips.sh {input.setOneDUP} {params.setTwoDUP} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DUP/SSm;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/SSm;\n"
        "bash ./Scripts/compare_breakends_w_truvari_trips.sh {input.setOneBND} {params.setTwoBND} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/BND"
SnakeMake From line 999 of Rules/truvari_bench_sv_files_ssm.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/SSm;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/SSm;\n"
        "bash ./Scripts/compare_breakends_w_truvari_quads.sh {params.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/SSm"
SnakeMake From line 1162 of Rules/truvari_bench_sv_files_ssm.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/SSm;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/SSm;\n"
        "bash ./Scripts/compare_breakends_w_truvari_quads.sh {params.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/SSm"
SnakeMake From line 1226 of Rules/truvari_bench_sv_files_ssm.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/SSm;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/SSm;\n"
        "bash ./Scripts/compare_breakends_w_truvari_quads.sh {params.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/SSm"
SnakeMake From line 1290 of Rules/truvari_bench_sv_files_ssm.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/SSm;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_quads.sh {params.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/SSm;\n"
        "bash ./Scripts/compare_breakends_w_truvari_quads.sh {params.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/SSm"
SnakeMake From line 1354 of Rules/truvari_bench_sv_files_ssm.smk 
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shell:
        "bash ./Scripts/compare_sv_files_w_truvari_all.sh {params.setOneDEL} {params.setTwoDEL} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/DEL/SSm;\n"
        "bash ./Scripts/compare_sv_files_w_truvari_all.sh {params.setOneINS} {params.setTwoINS} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INS/SSm;\n"
        "bash ./Scripts/compare_breakends_w_truvari_all.sh {params.setOneINV} {params.setTwoINV} {params.refGenome} {params.minSize} {params.maxSize} {params.minOverlap} {params.maxRefDist} {params.truvariDir}/{params.toolsPrefix}/INV/SSm"
SnakeMake From line 1435 of Rules/truvari_bench_sv_files_ssm.smk 
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shell:
        "bcftools filter -e \'REF ~ \"NNN*\" || ALT ~ \"NNN*\"\' -o {output.removedNs} {input};\n"
        "bcftools filter -e \'INFO/SVLEN<-{params.maxSize} || INFO/SVLEN>{params.maxSize} || INFO/RE<{params.minSupp}\' -o {output.finalFilter} {output.removedNs}"
SnakeMake BCFtools From line 15 of Rules/verify_sv_filtering.smk 
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shell:
        "bcftools filter -e \'REF ~ \"NNN*\" || ALT ~ \"NNN*\"\' -o {output.removedNs} {input};\n"
        "bcftools filter -e \'QUAL<{params.minMAPQ} || INFO/SVLEN<-{params.maxSize} || INFO/SVLEN>{params.maxSize} || INFO/SUPPORT<{params.minSupp}\' -o {output.finalFilter} {output.removedNs}"
SnakeMake BCFtools From line 33 of Rules/verify_sv_filtering.smk 
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shell:
        "bcftools filter -e \'SVTYPE == \"INV\" && ((INFO/END-POS)<-{params.maxSize} || (INFO/END-POS)>{params.maxSize})\' -o {output.filteredInv} {input};\n"
        "bcftools filter -e \'QUAL<{params.minMAPQ} || INFO/SVLEN<-{params.maxSize} || INFO/SVLEN>{params.maxSize} || (INFO/END-POS)<-{params.maxSize} || (INFO/END-POS)>{params.maxSize} || INFO/SUPPORT<{params.minSupp}\' -o {output.finalFilter} {output.filteredInv}"
SnakeMake BCFtools From line 51 of Rules/verify_sv_filtering.smk 
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shell:
        "bcftools filter -e \'REF ~ \"NNN*\" || ALT ~ \"NNN*\"\' -o {output.removedNs} {input};\n"
        "bcftools filter -e \'SVTYPE == \"INV\" && ((INFO/END-POS)<-{params.maxSize} || (INFO/END-POS)>{params.maxSize})\' -o {output.filteredInv} {output.removedNs};\n"
        "bcftools filter -e \'INFO/SVLEN<-{params.maxSize} || INFO/SVLEN>{params.maxSize}\' -o {output.finalFilter} {output.filteredInv}"
SnakeMake BCFtools From line 70 of Rules/verify_sv_filtering.smk 
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shell:
        "bcftools filter -e \'INFO/SVTYPE == \"SNV\"\' -o {params.tempFile1} {input};\n"
        "bcftools filter -e \'INFO/SVLEN<{params.minSize} && INFO/SVLEN>-{params.minSize}\' -o {params.tempFile2} {params.tempFile1};\n"
        "bcftools filter -e \'REF ~ \"NNN*\" || ALT ~ \"NNN*\"\' -o {output.removedNs} {params.tempFile2};\n"
        "bcftools filter -e \'INFO/SVLEN<-{params.maxSize} || INFO/SVLEN>{params.maxSize}\' -o {output.finalFilter} {output.removedNs};\n"
        "rm {params.tempFile1} {params.tempFile2}"
SnakeMake BCFtools From line 89 of Rules/verify_sv_filtering.smk 
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SV_DIR=$1
shift #remove output file as first arg so remainder can be added to bcftools command (concats all files provided after output)
COMBO_EXTENT=$1
shift

TP_FILEs=""
for FILE in $*
do
	#bcftools sort -o $DIR/tp.sorted.vcf $DIR/tp.vcf
	bgzip -c $FILE > $FILE.gz
	tabix $FILE.gz
	TP_FILES="$FILE.gz $TP_FILES"
done

#Ensure parent directories set up before bcftools execution
mkdir -p $SV_DIR

#Aggregate and sort remaining input files
echo "Combining VCF files for each type to $OUTPUT_FILE!.."
bcftools concat --allow-overlaps --remove-duplicates -o $SV_DIR/tp.$COMBO_EXTENT.vcf -O v `echo $TP_FILES`
bcftools sort -o $SV_DIR/tp.$COMBO_EXTENT.sorted.vcf $SV_DIR/tp.$COMBO_EXTENT.vcf
echo "Job's done!.."
Shell BCFtools tabix From line 3 of Scripts/aggregate_truvari_tp_files_no_dups.sh 
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THREADS=$1
Z_DROP=$2
PRESET_VAL=$3
REF_GENOME=$4
OUTPUT_FILE=$5
ALIGN_DIR=$6
READS_DIR=$7
READS_LIST=$8

echo "Starting Minimap2 Alignment..."
mkdir -p $ALIGN_DIR

#Extract all target read files' Accessions from provided list file
READ_INPUT_FILES=""
readarray ACCESSIONS_ARRAY < $READS_LIST
for ACCESSION in "${ACCESSIONS_ARRAY[@]}"
do
	READ_INPUT_FILES="${READS_DIR}/$(echo $ACCESSION | tr -d "\n").fastq $READ_INPUT_FILES"
done

minimap2 -t $THREADS --MD -a -z $Z_DROP -x $PRESET_VAL -Y $REF_GENOME $READ_INPUT_FILES > $OUTPUT_FILE
echo "Alignment complete!.."
Shell Minimap2 From line 3 of Scripts/align_reads_w_minimap2.sh 
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TOOL_A=$1
shift
TOOL_B=$1
shift
SV_TYPE=$1
shift
OUTPUT_FILE=$1
shift
WRITE_MODE=$1 #"W" for overwrite or "A" for append
shift

INTERSECTION_SIZE="0"
TOOL_A_SIZE="0"
TOOL_B_SIZE="0"
TOOL_A_UNIQUE="0"
TOOL_B_UNIQUE="0"

for TRUVARI_SUMMARY in $*
do
	#Confirm existance of Truvari result file before running calculations
	if [ ! -f "$TRUVARI_SUMMARY" ]; then
		echo "Error reading $TRUVARI_SUMMARY! Terminating..."
	fi

	#Get size of each set contained in files (extract the numeric value in truvari summary.txt from a specific line containing an identifier)
	#Shared/Common values
	INTERSECTION_SIZE=$(( INTERSECTION_SIZE+$(cat $TRUVARI_SUMMARY | grep "TP-base.:" | tr -cd [0-9.]) ))

	#Tool A's values
	TOOL_A_SIZE=$(( TOOL_A_SIZE +  $(cat $TRUVARI_SUMMARY | grep "base cnt" | tr -cd [0-9.]) ))
	TOOL_A_UNIQUE=$(( TOOL_A_UNIQUE + $(cat $TRUVARI_SUMMARY | grep "FN.:" | tr -cd [0-9.]) ))

	#Tool B's values
	TOOL_B_SIZE=$(( TOOL_B_SIZE + $(cat $TRUVARI_SUMMARY | grep "call cnt" | tr -cd [0-9.]) ))
	TOOL_B_UNIQUE=$(( TOOL_B_UNIQUE + $(cat $TRUVARI_SUMMARY | grep "FP.:" | tr -cd [0-9.]) ))
done

#Calculate Precision rates for pair of tools based on sums produced
#TOOL_A_PRECISION=$(awk -v INTERSECT="$INTERSECTION_SIZE" -v ASIZE="$TOOL_A_SIZE" 'BEGIN { printf "%.2f", INTERSECT/ASIZE*100 }' </dev/null)
TOOL_A_PRECISION=$(awk -v INTERSECT="$INTERSECTION_SIZE" -v ASIZE="$TOOL_A_SIZE" 'BEGIN { printf "%.2f", (ASIZE>0) ? INTERSECT/ASIZE*100 : 0.0 }' </dev/null)
if [ -z ${TOOL_A_PRECISION} ]; then
	TOOL_A_PRECISION="0.0"
fi

#TOOL_B_PRECISION=$(awk -v INTERSECT="$INTERSECTION_SIZE" -v BSIZE="$TOOL_B_SIZE" 'BEGIN { printf "%.2f", INTERSECT/BSIZE*100 }' </dev/null)
TOOL_B_PRECISION=$(awk -v INTERSECT="$INTERSECTION_SIZE" -v BSIZE="$TOOL_B_SIZE" 'BEGIN { printf "%.2f", (BSIZE>0)? INTERSECT/BSIZE*100 : 0.0 }' </dev/null)
if [ -z ${TOOL_B_PRECISION} ]; then
	TOOL_B_PRECISION="0.0"
fi

#Calculate union size and Jaccard Index value for the provided pair of tools
UNION_SIZE=$((INTERSECTION_SIZE+TOOL_A_UNIQUE+TOOL_B_UNIQUE))
if [ -z ${UNION_SIZE} ]; then
	UNION_SIZE="0.0"
fi

#JACCARD=$(awk -v INTERSECT="$INTERSECTION_SIZE" -v UNION="$UNION_SIZE" 'BEGIN { printf "%.2f", INTERSECT/UNION*100 }' </dev/null)
JACCARD=$(awk -v INTERSECT="$INTERSECTION_SIZE" -v UNION="$UNION_SIZE" 'BEGIN { printf "%.2f",  (UNION>0)? INTERSECT/UNION*100 : 0.0 }' </dev/null)
if [ -z ${JACCARD} ]; then
	JACCARD="0.0"
fi

#Check if script should write/overwrite a file with the new header info (should only be done for first pair of tools compared)
if [ "$WRITE_MODE" = "W" ] || [ "$WRITE_MODE" = "w" ]
then
       #echo "#ToolA    ToolB   Type    Jaccard%        PrecA        PrecB        Union# SizeA   SizeB   UniqueA Intersect       UniqueB" > $OUTPUT_FILE
	echo -e "ToolA\tToolB\tType\tSizeA\tSizeB\tUniqueA\tUniqueB\tIntersect\tUnion\tOverlapA\tOverlapB\tJaccard" > "$OUTPUT_FILE"
fi

#Append the entry for the pair of tools designated by arguments
#echo "$TOOL_A   $TOOL_B $SV_TYPE        ${JACCARD}%        ${TOOL_A_PRECISION}%       ${TOOL_B_PRECISION}%       $UNION_SIZE     $TOOL_A_SIZE    $TOOL_B_SIZE    $TOOL_A_UNIQUE  $INTERSECTION_SIZE      $TOOL_B_UNIQUE" >> "$OUTPUT_FILE"
echo -e "$TOOL_A\t$TOOL_B\t$SV_TYPE\t$TOOL_A_SIZE\t$TOOL_B_SIZE\t$TOOL_A_UNIQUE\t$TOOL_B_UNIQUE\t$INTERSECTION_SIZE\t$UNION_SIZE\t${TOOL_A_PRECISION}%\t${TOOL_B_PRECISION}%\t${JACCARD}%" >> "$OUTPUT_FILE"
Shell From line 3 of Scripts/calculate_iou_from_truvari_list.sh 
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TOOL_A=$1
TOOL_B=$2
SV_TYPE=$3
TRUVARI_SUMMARY=$4
OUTPUT_FILE=$5
WRITE_MODE=$6 #"W" for overwrite or "A" for append

#Confirm existance of Truvari result file before running calculations
if [ ! -f "$TRUVARI_SUMMARY" ]; then
	echo "Error reading $TRUVARI_SUMMARY! Terminating..."
fi

#Get size of each set contained in files (extract the numeric value in truvari summary.txt from a specific line containing an identifier)
#Shared/Common values
INTERSECTION_SIZE=$(cat $TRUVARI_SUMMARY | grep "TP-base.:" | tr -cd [0-9.])

#Tool A's values
TOOL_A_SIZE=$(cat $TRUVARI_SUMMARY | grep "base cnt" | tr -cd [0-9.])
TOOL_A_PRECISION=$(cat $TRUVARI_SUMMARY | grep "recall" | tr -cd [0-9.])
TOOL_A_PRECISION=$(awk -v APRECISION="$TOOL_A_PRECISION" 'BEGIN { printf "%.2f", APRECISION*100 }' </dev/null)
if [ -z ${TOOL_A_PRECISION} ]; then
        TOOL_A_PRECISION="0.0"
fi
TOOL_A_UNIQUE=$(cat $TRUVARI_SUMMARY | grep "FN.:" | tr -cd [0-9.])

#Tool B's values
TOOL_B_SIZE=$(cat $TRUVARI_SUMMARY | grep "call cnt" | tr -cd [0-9.])
TOOL_B_PRECISION=$(cat $TRUVARI_SUMMARY | grep "precision" | tr -cd [0-9.])
TOOL_B_PRECISION=$(awk -v BPRECISION="$TOOL_B_PRECISION" 'BEGIN { printf "%.2f", BPRECISION*100 }' </dev/null)
if [ -z ${TOOL_B_PRECISION} ]; then
        TOOL_B_PRECISION="0.0"
fi
TOOL_B_UNIQUE=$(cat $TRUVARI_SUMMARY | grep "FP.:" | tr -cd [0-9.])

#Calculate union size and Jaccard Index value for the provided pair of tools
UNION_SIZE=$((INTERSECTION_SIZE+TOOL_A_UNIQUE+TOOL_B_UNIQUE))
if [ -z ${UNION_SIZE} ]; then
	UNION_SIZE="0.0"
fi

#JACCARD=$(awk -v INTERSECT="$INTERSECTION_SIZE" -v UNION="$UNION_SIZE" 'BEGIN { printf "%.2f", INTERSECT/UNION*100 }' </dev/null)
JACCARD=$(awk -v INTERSECT="$INTERSECTION_SIZE" -v UNION="$UNION_SIZE" 'BEGIN { printf "%.2f",  (UNION>0)? INTERSECT/UNION*100 : 0.0 }' </dev/null)
if [ -z ${JACCARD} ]; then
        JACCARD="0.0"
fi

#Check if script should write/overwrite a file with the new header info (should only be done for first pair of tools compared)
if [ "$WRITE_MODE" = "W" ] || [ "$WRITE_MODE" = "w" ]
then
       #echo "#ToolA    ToolB   Type    Jaccard%        PrecA        PrecB        Union# SizeA   SizeB   UniqueA Intersect       UniqueB" > $OUTPUT_FILE
        echo -e "ToolA\tToolB\tType\tSizeA\tSizeB\tUniqueA\tUniqueB\tIntersect\tUnion\tOverlapA\tOverlapB\tJaccard" > "$OUTPUT_FILE"
fi

#Append the entry for the pair of tools designated by arguments
#echo "$TOOL_A   $TOOL_B $SV_TYPE        ${JACCARD}%        ${TOOL_A_PRECISION}%       ${TOOL_B_PRECISION}%       $UNION_SIZE     $TOOL_A_SIZE    $TOOL_B_SIZE    $TOOL_A_UNIQUE  $INTERSECTION_SIZE      $TOOL_B_UNIQUE" >> "$OUTPUT_FILE"
echo -e "$TOOL_A\t$TOOL_B\t$SV_TYPE\t$TOOL_A_SIZE\t$TOOL_B_SIZE\t$TOOL_A_UNIQUE\t$TOOL_B_UNIQUE\t$INTERSECTION_SIZE\t$UNION_SIZE\t${TOOL_A_PRECISION}%\t${TOOL_B_PRECISION}%\t${JACCARD}%" >> "$OUTPUT_FILE"
Shell From line 3 of Scripts/calculate_iou_from_truvari_pair.sh 
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INPUT_FILE=$1
TOOL_A=$2
TOOL_B=$3
SV_TYPE="ALL"

#ToolA   ToolB   Type    SizeA   SizeB   UniqueA UniqueB Intersect       Union   OverlapA        OverlapB        Jaccard

#Get size of each set contained in rows
#Shared/Common values
INTERSECTION_SIZE=$(awk '{sum+=$8;} END{print sum;}' $INPUT_FILE)

#Tool A's values
TOOL_A_SIZE=$(awk '{sum+=$4;} END{print sum;}' $INPUT_FILE)
#TOOL_A_PRECISION=$(awk -v INTERSECT="$INTERSECTION_SIZE" -v ASIZE="$TOOL_A_SIZE" 'BEGIN { printf "%.2f", INTERSECT/ASIZE*100 }' </dev/null)
TOOL_A_PRECISION=$(awk -v INTERSECT="$INTERSECTION_SIZE" -v ASIZE="$TOOL_A_SIZE" 'BEGIN { printf "%.2f", (ASIZE>0) ? INTERSECT/ASIZE*100 : 0.0 }' </dev/null)
if [ -z ${TOOL_A_PRECISION} ]; then
	echo "Precision A missing"
        TOOL_A_PRECISION="0.0"
fi
TOOL_A_UNIQUE=$(awk '{sum+=$6;} END{print sum;}' $INPUT_FILE)

#Tool B's values
TOOL_B_SIZE=$(awk '{sum+=$5;} END{print sum;}' $INPUT_FILE)
#TOOL_B_PRECISION=$(awk -v INTERSECT="$INTERSECTION_SIZE" -v BSIZE="$TOOL_B_SIZE" 'BEGIN { printf "%.2f", INTERSECT/BSIZE*100 }' </dev/null)
TOOL_B_PRECISION=$(awk -v INTERSECT="$INTERSECTION_SIZE" -v BSIZE="$TOOL_B_SIZE" 'BEGIN { printf "%.2f", (BSIZE>0) ? INTERSECT/BSIZE*100 : 0.0 }' </dev/null)
if [ -z ${TOOL_B_PRECISION} ]; then
	echo "Precision B missing"
        TOOL_B_PRECISION="0.0"
fi
TOOL_B_UNIQUE=$(awk '{sum+=$7;} END{print sum;}' $INPUT_FILE)

#Calculate union size and Jaccard Index value for the provided pair of tools
UNION_SIZE=$((INTERSECTION_SIZE+TOOL_A_UNIQUE+TOOL_B_UNIQUE))
if [ -z ${UNION_SIZE} ]; then
	echo "Union missing"
	UNION_SIZE="0.0"
fi

#JACCARD=$(awk -v INTERSECT="$INTERSECTION_SIZE" -v UNION="$UNION_SIZE" 'BEGIN { printf "%.2f", INTERSECT/UNION*100 }' </dev/null)
JACCARD=$(awk -v INTERSECT="$INTERSECTION_SIZE" -v UNION="$UNION_SIZE" 'BEGIN { printf "%.2f", (UNION>0) ? INTERSECT/UNION*100 : 0.0 }' </dev/null)
if [ -z ${JACCARD} ]; then
	echo "Jaccard missing"
        JACCARD="0.0"
fi

#Append the entry for the pair of tools designated by arguments
#echo "$TOOL_A	$TOOL_B	$SV_TYPE	${JACCARD}%	${TOOL_A_PRECISION}%	${TOOL_B_PRECISION}%	$UNION_SIZE	$TOOL_A_SIZE	$TOOL_B_SIZE	$TOOL_A_UNIQUE	$INTERSECTION_SIZE	$TOOL_B_UNIQUE" >> $INPUT_FILE
echo -e "$TOOL_A\t$TOOL_B\t$SV_TYPE\t$TOOL_A_SIZE\t$TOOL_B_SIZE\t$TOOL_A_UNIQUE\t$TOOL_B_UNIQUE\t$INTERSECTION_SIZE\t$UNION_SIZE\t${TOOL_A_PRECISION}%\t${TOOL_B_PRECISION}%\t${JACCARD}%" >> "$INPUT_FILE"
Shell From line 3 of Scripts/calculate_total_from_tsv.sh 
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TRUVARI_DIR=$1
shift #remove output file as first arg so remainder can be added to bcftools command (concats all files provided after output)

TP_CALL_FILES=""
TP_BASE_FILES=""
FP_FILES=""
FN_FILES=""
for DIR in $*
do
	bcftools sort -o $DIR/tp-call.sorted.vcf $DIR/tp-call.vcf
	bgzip -c $DIR/tp-call.sorted.vcf > $DIR/tp-call.sorted.vcf.gz
	tabix $DIR/tp-call.sorted.vcf.gz
	TP_CALL_FILES="$DIR/tp-call.sorted.vcf.gz $TP_CALL_FILES"

        bcftools sort -o $DIR/tp-base.sorted.vcf $DIR/tp-base.vcf
        bgzip -c $DIR/tp-base.sorted.vcf > $DIR/tp-base.sorted.vcf.gz
        tabix $DIR/tp-base.sorted.vcf.gz
        TP_BASE_FILES="$DIR/tp-base.sorted.vcf.gz $TP_BASE_FILES"

        bcftools sort -o $DIR/fp.sorted.vcf $DIR/fp.vcf
        bgzip -c $DIR/fp.sorted.vcf > $DIR/fp.sorted.vcf.gz
        tabix $DIR/fp.sorted.vcf.gz
        FP_FILES="$DIR/fp.sorted.vcf.gz $FP_FILES"

        bcftools sort -o $DIR/fn.sorted.vcf $DIR/fn.vcf
        bgzip -c $DIR/fn.sorted.vcf > $DIR/fn.sorted.vcf.gz
        tabix $DIR/fn.sorted.vcf.gz
        FN_FILES="$DIR/fn.sorted.vcf.gz $FN_FILES"
done

echo "Combining VCF files for each type to $OUTPUT_FILE!.."
bcftools concat --allow-overlaps -o $TRUVARI_DIR/tp-call.vcf -O v `echo $TP_CALL_FILES`
bcftools sort -o $TRUVARI_DIR/tp-call.sorted.vcf $TRUVARI_DIR/tp-call.vcf
bcftools concat --allow-overlaps -o $TRUVARI_DIR/tp-base.vcf -O v `echo $TP_BASE_FILES`
bcftools sort -o $TRUVARI_DIR/tp-base.sorted.vcf $TRUVARI_DIR/tp-base.vcf
bcftools concat --allow-overlaps -o $TRUVARI_DIR/fp.vcf -O v `echo $FP_FILES`
bcftools sort -o $TRUVARI_DIR/fp.sorted.vcf $TRUVARI_DIR/fp.vcf
bcftools concat --allow-overlaps -o $TRUVARI_DIR/fn.vcf -O v `echo $FN_FILES`
bcftools sort -o $TRUVARI_DIR/fn.sorted.vcf $TRUVARI_DIR/fn.vcf
echo "Job's done!.."
Shell BCFtools tabix From line 3 of Scripts/combine_vcf_files_basic.sh 
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TRUVARI_DIR_A=$1
TRUVARI_DIR_B=$2
REF_GENOME=$3
MIN_SIZE=$4
MAX_SIZE=$5
OVERLAP=$6
MAX_REF_DIST=$7
OUTPUT_DIR=$8

#Truvari requires sorted, zipped, and indexed VCF files as input. (Re)Generate files before starting Truvari bench
bcftools sort -o ${TRUVARI_DIR_A}/tp-call.sorted.vcf $TRUVARI_DIR_A/tp-call.vcf
bgzip -c ${TRUVARI_DIR_A}/tp-call.sorted.vcf > ${TRUVARI_DIR_A}/tp-call.sorted.vcf.gz
tabix ${TRUVARI_DIR_A}/tp-call.sorted.vcf.gz

bcftools sort -o ${TRUVARI_DIR_A}/tp-base.sorted.vcf $TRUVARI_DIR_A/tp-base.vcf
bgzip -c ${TRUVARI_DIR_A}/tp-base.sorted.vcf > ${TRUVARI_DIR_A}/tp-base.sorted.vcf.gz
tabix ${TRUVARI_DIR_A}/tp-base.sorted.vcf.gz


bcftools sort -o ${TRUVARI_DIR_B}/FromTPCall/tp-call.sorted.vcf $TRUVARI_DIR_B/FromTPCall/tp-call.vcf
bgzip -c ${TRUVARI_DIR_B}/FromTPCall/tp-call.sorted.vcf > ${TRUVARI_DIR_B}/FromTPCall/tp-call.sorted.vcf.gz
tabix ${TRUVARI_DIR_B}/FromTPCall/tp-call.sorted.vcf.gz

bcftools sort -o ${TRUVARI_DIR_B}/FromTPCall/tp-base.sorted.vcf $TRUVARI_DIR_B/FromTPCall/tp-base.vcf
bgzip -c ${TRUVARI_DIR_B}/FromTPCall/tp-base.sorted.vcf > ${TRUVARI_DIR_B}/FromTPCall/tp-base.sorted.vcf.gz
tabix ${TRUVARI_DIR_B}/FromTPCall/tp-base.sorted.vcf.gz


#bcftools sort -o ${TRUVARI_DIR_B}/FromTPBase/tp-call.sorted.vcf $TRUVARI_DIR_B/FromTPBase/tp-call.vcf
#bgzip -c ${TRUVARI_DIR_B}/FromTPBase/tp-call.sorted.vcf > ${TRUVARI_DIR_B}/FromTPBase/tp-call.sorted.vcf.gz
#tabix ${TRUVARI_DIR_B}/FromTPBase/tp-call.sorted.vcf.gz

#bcftools sort -o ${TRUVARI_DIR_B}/FromTPBase/tp-base.sorted.vcf $TRUVARI_DIR_B/FromTPBase/tp-base.vcf
#bgzip -c ${TRUVARI_DIR_B}/FromTPBase/tp-base.sorted.vcf > ${TRUVARI_DIR_B}/FromTPBase/tp-base.sorted.vcf.gz
#tabix ${TRUVARI_DIR_B}/FromTPBase/tp-base.sorted.vcf.gz

#Ensure parent directories set up before Truvari execution
mkdir -p $OUTPUT_DIR/Call
mkdir -p $OUTPUT_DIR/Base

#Truvari creates the output directory during execution and won't overwrite an existing directory. Remove target $OUTPUT_DIR if it already exists.
if [ -d $OUTPUT_DIR/Call/FromTPCall ]
then
	echo "$OUTPUT_DIR already exists! Removing to allow truvari to run!.. "
	rm -r $OUTPUT_DIR/Call/FromTPCall
fi

if [ -d $OUTPUT_DIR/Call/FromTPBase ]
then
        echo "$OUTPUT_DIR already exists! Removing to allow truvari to run!.. "
        rm -r $OUTPUT_DIR/Call/FromTPBase
fi

if [ -d $OUTPUT_DIR/Base/FromTPCall ]
then
        echo "$OUTPUT_DIR already exists! Removing to allow truvari to run!.. "
        rm -r $OUTPUT_DIR/Base/FromTPCall
fi

if [ -d $OUTPUT_DIR/Base/FromTPBase ]
then
        echo "$OUTPUT_DIR already exists! Removing to allow truvari to run!.. "
        rm -r $OUTPUT_DIR/Base/FromTPBase
fi

#Execute Truvari Bench to compare the VCF files provided in the script's arguments
truvari bench -o $OUTPUT_DIR/Call/FromTPCall -f $REF_GENOME -b ${TRUVARI_DIR_A}/tp-call.sorted.vcf.gz -c ${TRUVARI_DIR_B}/FromTPCall/tp-call.sorted.vcf.gz -s 0 -S 0 --sizemax $MAX_SIZE -r $MAX_REF_DIST -p 0 -P $OVERLAP -C $MAX_REF_DIST
truvari bench -o $OUTPUT_DIR/Call/FromTPBase -f $REF_GENOME -b ${TRUVARI_DIR_A}/tp-call.sorted.vcf.gz -c ${TRUVARI_DIR_B}/FromTPCall/tp-base.sorted.vcf.gz -s 0 -S 0 --sizemax $MAX_SIZE -r $MAX_REF_DIST -p 0 -P $OVERLAP -C $MAX_REF_DIST
truvari bench -o $OUTPUT_DIR/Base/FromTPCall -f $REF_GENOME -b ${TRUVARI_DIR_A}/tp-base.sorted.vcf.gz -c ${TRUVARI_DIR_B}/FromTPCall/tp-call.sorted.vcf.gz -s 0 -S 0 --sizemax $MAX_SIZE -r $MAX_REF_DIST -p 0 -P $OVERLAP -C $MAX_REF_DIST
Shell BCFtools tabix From line 3 of Scripts/compare_breakends_w_truvari_all.sh 
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SV_FILE_A=$1
SV_FILE_B=$2
REF_GENOME=$3
MIN_SIZE=$4
MAX_SIZE=$5
OVERLAP=$6
MAX_REF_DIST=$7
OUTPUT_DIR=$8

#Truvari requires sorted, zipped, and indexed VCF files as input. (Re)Generate files before starting Truvari bench
bcftools sort -o ${SV_FILE_A}.sorted $SV_FILE_A
bgzip -c ${SV_FILE_A}.sorted > ${SV_FILE_A}.gz
tabix ${SV_FILE_A}.gz

bcftools sort -o ${SV_FILE_B}.sorted $SV_FILE_B
bgzip -c ${SV_FILE_B}.sorted > ${SV_FILE_B}.gz
tabix ${SV_FILE_B}.gz

#Truvari creates the output directory during execution and won't overwrite an existing directory. Remove target $OUTPUT_DIR if it already exists.
mkdir -p $OUTPUT_DIR
if [ -d $OUTPUT_DIR ]
then
	echo "$OUTPUT_DIR already exists! Removing to allow truvari to run!.. "
	rm -r $OUTPUT_DIR
fi

#Execute Truvari Bench to compare the VCF files provided in the script's arguments
truvari bench -o $OUTPUT_DIR -f $REF_GENOME -b ${SV_FILE_A}.gz -c ${SV_FILE_B}.gz -s 0 -S 0 --sizemax $MAX_SIZE -r $MAX_REF_DIST -p 0 -P $OVERLAP -C $MAX_REF_DIST
Shell BCFtools tabix From line 3 of Scripts/compare_breakends_w_truvari_pairs.sh 
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TRUVARI_DIR_A=$1
TRUVARI_DIR_B=$2
REF_GENOME=$3
MIN_SIZE=$4
MAX_SIZE=$5
OVERLAP=$6
MAX_REF_DIST=$7
OUTPUT_DIR=$8

#Truvari requires sorted, zipped, and indexed VCF files as input. (Re)Generate files before starting Truvari bench
bcftools sort -o ${TRUVARI_DIR_A}/tp-call.sorted.vcf $TRUVARI_DIR_A/tp-call.vcf
bgzip -c ${TRUVARI_DIR_A}/tp-call.sorted.vcf > ${TRUVARI_DIR_A}/tp-call.sorted.vcf.gz
tabix ${TRUVARI_DIR_A}/tp-call.sorted.vcf.gz

bcftools sort -o ${TRUVARI_DIR_A}/tp-base.sorted.vcf $TRUVARI_DIR_A/tp-base.vcf
bgzip -c ${TRUVARI_DIR_A}/tp-base.sorted.vcf > ${TRUVARI_DIR_A}/tp-base.sorted.vcf.gz
tabix ${TRUVARI_DIR_A}/tp-base.sorted.vcf.gz

bcftools sort -o ${TRUVARI_DIR_B}/tp-call.sorted.vcf $TRUVARI_DIR_B/tp-call.vcf
bgzip -c ${TRUVARI_DIR_B}/tp-call.sorted.vcf > ${TRUVARI_DIR_B}/tp-call.sorted.vcf.gz
tabix ${TRUVARI_DIR_B}/tp-call.sorted.vcf.gz

bcftools sort -o ${TRUVARI_DIR_B}/tp-base.sorted.vcf $TRUVARI_DIR_B/tp-base.vcf
bgzip -c ${TRUVARI_DIR_B}/tp-base.sorted.vcf > ${TRUVARI_DIR_B}/tp-base.sorted.vcf.gz
tabix ${TRUVARI_DIR_B}/tp-base.sorted.vcf.gz

#Ensure required parent directories are set up before execution
mkdir -p $OUTPUT_DIR/Call
mkdir -p $OUTPUT_DIR/Base

#Truvari creates the output directory during execution and won't overwrite an existing directory. Remove target $OUTPUT_DIR if it already exists.
if [ -d $OUTPUT_DIR/Call/FromTPCall ]
then
	echo "Output Dir already exists! Removing to allow truvari to run!.. "
	rm -r $OUTPUT_DIR/Call/FromTPCall
fi

if [ -d $OUTPUT_DIR/Call/FromTPBase ]
then
        echo "Output Dir already exists! Removing to allow truvari to run!.. "
        rm -r $OUTPUT_DIR/Call/FromTPBase
fi

if [ -d $OUTPUT_DIR/Base/FromTPCall ]
then
        echo "Output Dir already exists! Removing to allow truvari to run!.. "
        rm -r $OUTPUT_DIR/Base/FromTPCall
fi

if [ -d $OUTPUT_DIR/Base/FromTPBase ]
then
        echo "Output Dir already exists! Removing to allow truvari to run!.. "
        rm -r $OUTPUT_DIR/Base/FromTPBase
fi

#Execute Truvari Bench to compare the VCF files provided in the script's arguments
truvari bench -o $OUTPUT_DIR/Call/FromTPCall -f $REF_GENOME -b ${TRUVARI_DIR_A}/tp-call.sorted.vcf.gz -c ${TRUVARI_DIR_B}/tp-call.sorted.vcf.gz -s 0 -S 0 --sizemax $MAX_SIZE -r $MAX_REF_DIST -p 0 -P $OVERLAP -C $MAX_REF_DIST
truvari bench -o $OUTPUT_DIR/Call/FromTPBase -f $REF_GENOME -b ${TRUVARI_DIR_A}/tp-call.sorted.vcf.gz -c ${TRUVARI_DIR_B}/tp-base.sorted.vcf.gz -s 0 -S 0 --sizemax $MAX_SIZE -r $MAX_REF_DIST -p 0 -P $OVERLAP -C $MAX_REF_DIST
truvari bench -o $OUTPUT_DIR/Base/FromTPCall -f $REF_GENOME -b ${TRUVARI_DIR_A}/tp-base.sorted.vcf.gz -c ${TRUVARI_DIR_B}/tp-call.sorted.vcf.gz -s 0 -S 0 --sizemax $MAX_SIZE -r $MAX_REF_DIST -p 0 -P $OVERLAP -C $MAX_REF_DIST
Shell BCFtools tabix From line 3 of Scripts/compare_breakends_w_truvari_quads.sh 
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SV_FILE_A=$1
TRUVARI_DIR=$2
REF_GENOME=$3
MIN_SIZE=$4
MAX_SIZE=$5
OVERLAP=$6
MAX_REF_DIST=$7
OUTPUT_DIR=$8

#Truvari requires sorted, zipped, and indexed VCF files as input. (Re)Generate files before starting Truvari bench
bcftools sort -o ${SV_FILE_A}.sorted $SV_FILE_A
bgzip -c ${SV_FILE_A}.sorted > ${SV_FILE_A}.gz
tabix ${SV_FILE_A}.gz

bcftools sort -o ${TRUVARI_DIR}/tp-call.sorted.vcf $TRUVARI_DIR/tp-call.vcf
bgzip -c ${TRUVARI_DIR}/tp-call.sorted.vcf > ${TRUVARI_DIR}/tp-call.sorted.vcf.gz
tabix ${TRUVARI_DIR}/tp-call.sorted.vcf.gz

bcftools sort -o ${TRUVARI_DIR}/tp-base.sorted.vcf $TRUVARI_DIR/tp-base.vcf
bgzip -c ${TRUVARI_DIR}/tp-base.sorted.vcf > ${TRUVARI_DIR}/tp-base.sorted.vcf.gz
tabix ${TRUVARI_DIR}/tp-base.sorted.vcf.gz

#Ensure Parent directories are set up before Truvari execution
mkdir -p $OUTPUT_DIR

#Truvari creates the output directory during execution and won't overwrite an existing directory. Remove target $OUTPUT_DIR if it already exists.
if [ -d $OUTPUT_DIR/FromTPCall ]
then
	echo "Output Dir already exists! Removing to allow truvari to run!.. "
	rm -r $OUTPUT_DIR/FromTPCall
fi

if [ -d $OUTPUT_DIR/FromTPBase ]
then
        echo "Output Dir already exists! Removing to allow truvari to run!.. "
        rm -r $OUTPUT_DIR/FromTPBase
fi

#Execute Truvari Bench to compare the VCF files provided in the script's arguments
truvari bench -o $OUTPUT_DIR/FromTPCall -f $REF_GENOME -b ${SV_FILE_A}.gz -c ${TRUVARI_DIR}/tp-call.sorted.vcf.gz -s 0 -S 0 --sizemax $MAX_SIZE -r $MAX_REF_DIST -p 0 -P $OVERLAP -C $MAX_REF_DIST
truvari bench -o $OUTPUT_DIR/FromTPBase -f $REF_GENOME -b ${SV_FILE_A}.gz -c ${TRUVARI_DIR}/tp-base.sorted.vcf.gz -s 0 -S 0 --sizemax $MAX_SIZE -r $MAX_REF_DIST -p 0 -P $OVERLAP -C $MAX_REF_DIST
Shell BCFtools tabix From line 3 of Scripts/compare_breakends_w_truvari_trips.sh 
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TRUVARI_DIR_A=$1
TRUVARI_DIR_B=$2
REF_GENOME=$3
MIN_SIZE=$4
MAX_SIZE=$5
OVERLAP=$6
MAX_REF_DIST=$7
OUTPUT_DIR=$8

#Truvari requires sorted, zipped, and indexed VCF files as input. (Re)Generate files before starting Truvari bench
bcftools sort -o ${TRUVARI_DIR_A}/tp-call.sorted.vcf $TRUVARI_DIR_A/tp-call.vcf
bgzip -c ${TRUVARI_DIR_A}/tp-call.sorted.vcf > ${TRUVARI_DIR_A}/tp-call.sorted.vcf.gz
tabix ${TRUVARI_DIR_A}/tp-call.sorted.vcf.gz

bcftools sort -o ${TRUVARI_DIR_A}/tp-base.sorted.vcf $TRUVARI_DIR_A/tp-base.vcf
bgzip -c ${TRUVARI_DIR_A}/tp-base.sorted.vcf > ${TRUVARI_DIR_A}/tp-base.sorted.vcf.gz
tabix ${TRUVARI_DIR_A}/tp-base.sorted.vcf.gz


bcftools sort -o ${TRUVARI_DIR_B}/FromTPCall/tp-call.sorted.vcf $TRUVARI_DIR_B/FromTPCall/tp-call.vcf
bgzip -c ${TRUVARI_DIR_B}/FromTPCall/tp-call.sorted.vcf > ${TRUVARI_DIR_B}/FromTPCall/tp-call.sorted.vcf.gz
tabix ${TRUVARI_DIR_B}/FromTPCall/tp-call.sorted.vcf.gz

bcftools sort -o ${TRUVARI_DIR_B}/FromTPCall/tp-base.sorted.vcf $TRUVARI_DIR_B/FromTPCall/tp-base.vcf
bgzip -c ${TRUVARI_DIR_B}/FromTPCall/tp-base.sorted.vcf > ${TRUVARI_DIR_B}/FromTPCall/tp-base.sorted.vcf.gz
tabix ${TRUVARI_DIR_B}/FromTPCall/tp-base.sorted.vcf.gz


#bcftools sort -o ${TRUVARI_DIR_B}/FromTPBase/tp-call.sorted.vcf $TRUVARI_DIR_B/FromTPBase/tp-call.vcf
#bgzip -c ${TRUVARI_DIR_B}/FromTPBase/tp-call.sorted.vcf > ${TRUVARI_DIR_B}/FromTPBase/tp-call.sorted.vcf.gz
#tabix ${TRUVARI_DIR_B}/FromTPBase/tp-call.sorted.vcf.gz

#bcftools sort -o ${TRUVARI_DIR_B}/FromTPBase/tp-base.sorted.vcf $TRUVARI_DIR_B/FromTPBase/tp-base.vcf
#bgzip -c ${TRUVARI_DIR_B}/FromTPBase/tp-base.sorted.vcf > ${TRUVARI_DIR_B}/FromTPBase/tp-base.sorted.vcf.gz
#tabix ${TRUVARI_DIR_B}/FromTPBase/tp-base.sorted.vcf.gz

#Ensure parent directories set up before Truvari execution
mkdir -p $OUTPUT_DIR/Call
mkdir -p $OUTPUT_DIR/Base

#Truvari creates the output directory during execution and won't overwrite an existing directory. Remove target $OUTPUT_DIR if it already exists.
if [ -d $OUTPUT_DIR/Call/FromTPCall ]
then
	echo "$OUTPUT_DIR already exists! Removing to allow truvari to run!.. "
	rm -r $OUTPUT_DIR/Call/FromTPCall
fi

if [ -d $OUTPUT_DIR/Call/FromTPBase ]
then
        echo "$OUTPUT_DIR already exists! Removing to allow truvari to run!.. "
        rm -r $OUTPUT_DIR/Call/FromTPBase
fi

if [ -d $OUTPUT_DIR/Base/FromTPCall ]
then
        echo "$OUTPUT_DIR already exists! Removing to allow truvari to run!.. "
        rm -r $OUTPUT_DIR/Base/FromTPCall
fi

if [ -d $OUTPUT_DIR/Base/FromTPBase ]
then
        echo "$OUTPUT_DIR already exists! Removing to allow truvari to run!.. "
        rm -r $OUTPUT_DIR/Base/FromTPBase
fi

#Execute Truvari Bench to compare the VCF files provided in the script's arguments
truvari bench -o $OUTPUT_DIR/Call/FromTPCall -f $REF_GENOME -b ${TRUVARI_DIR_A}/tp-call.sorted.vcf.gz -c ${TRUVARI_DIR_B}/FromTPCall/tp-call.sorted.vcf.gz -s $MIN_SIZE --sizemax $MAX_SIZE -r $MAX_REF_DIST -p 0 -P $OVERLAP -C $MAX_REF_DIST
truvari bench -o $OUTPUT_DIR/Call/FromTPBase -f $REF_GENOME -b ${TRUVARI_DIR_A}/tp-call.sorted.vcf.gz -c ${TRUVARI_DIR_B}/FromTPCall/tp-base.sorted.vcf.gz -s $MIN_SIZE --sizemax $MAX_SIZE -r $MAX_REF_DIST -p 0 -P $OVERLAP -C $MAX_REF_DIST
truvari bench -o $OUTPUT_DIR/Base/FromTPCall -f $REF_GENOME -b ${TRUVARI_DIR_A}/tp-base.sorted.vcf.gz -c ${TRUVARI_DIR_B}/FromTPCall/tp-call.sorted.vcf.gz -s $MIN_SIZE --sizemax $MAX_SIZE -r $MAX_REF_DIST -p 0 -P $OVERLAP -C $MAX_REF_DIST
Shell BCFtools tabix From line 3 of Scripts/compare_sv_files_w_truvari_all.sh 
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SV_FILE_A=$1
SV_FILE_B=$2
REF_GENOME=$3
MIN_SIZE=$4
MAX_SIZE=$5
OVERLAP=$6
MAX_REF_DIST=$7
OUTPUT_DIR=$8

#Truvari requires sorted, zipped, and indexed VCF files as input. (Re)Generate files before starting Truvari bench
bcftools sort -o ${SV_FILE_A}.sorted $SV_FILE_A
bgzip -c ${SV_FILE_A}.sorted > ${SV_FILE_A}.gz
tabix ${SV_FILE_A}.gz

bcftools sort -o ${SV_FILE_B}.sorted $SV_FILE_B
bgzip -c ${SV_FILE_B}.sorted > ${SV_FILE_B}.gz
tabix ${SV_FILE_B}.gz

#Ensure parent directories set up before Truvari execution
mkdir -p $OUTPUT_DIR

#Truvari creates the output directory during execution and won't overwrite an existing directory. Remove target $OUTPUT_DIR if it already exists.
if [ -d $OUTPUT_DIR ]
then
	echo "$OUTPUT_DIR already exists! Removing to allow truvari to run!.. "
	rm -r $OUTPUT_DIR
fi

#Execute Truvari Bench to compare the VCF files provided in the script's arguments
truvari bench --typeignore -o $OUTPUT_DIR -f $REF_GENOME -b ${SV_FILE_A}.gz -c ${SV_FILE_B}.gz -s $MIN_SIZE --sizemax $MAX_SIZE -r $MAX_REF_DIST -p 0 -P $OVERLAP -C $MAX_REF_DIST
Shell BCFtools tabix From line 3 of Scripts/compare_sv_files_w_truvari_ignore_type_pairs.sh 
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TRUVARI_DIR_A=$1
TRUVARI_DIR_B=$2
REF_GENOME=$3
MIN_SIZE=$4
MAX_SIZE=$5
OVERLAP=$6
MAX_REF_DIST=$7
OUTPUT_DIR=$8

#Truvari requires sorted, zipped, and indexed VCF files as input. (Re)Generate files before starting Truvari bench
bcftools sort -o ${TRUVARI_DIR_A}/tp-call.sorted.vcf $TRUVARI_DIR_A/tp-call.vcf
bgzip -c ${TRUVARI_DIR_A}/tp-call.sorted.vcf > ${TRUVARI_DIR_A}/tp-call.sorted.vcf.gz
tabix ${TRUVARI_DIR_A}/tp-call.sorted.vcf.gz

bcftools sort -o ${TRUVARI_DIR_A}/tp-base.sorted.vcf $TRUVARI_DIR_A/tp-base.vcf
bgzip -c ${TRUVARI_DIR_A}/tp-base.sorted.vcf > ${TRUVARI_DIR_A}/tp-base.sorted.vcf.gz
tabix ${TRUVARI_DIR_A}/tp-base.sorted.vcf.gz

bcftools sort -o ${TRUVARI_DIR_B}/tp-call.sorted.vcf $TRUVARI_DIR_B/tp-call.vcf
bgzip -c ${TRUVARI_DIR_B}/tp-call.sorted.vcf > ${TRUVARI_DIR_B}/tp-call.sorted.vcf.gz
tabix ${TRUVARI_DIR_B}/tp-call.sorted.vcf.gz

bcftools sort -o ${TRUVARI_DIR_B}/tp-base.sorted.vcf $TRUVARI_DIR_B/tp-base.vcf
bgzip -c ${TRUVARI_DIR_B}/tp-base.sorted.vcf > ${TRUVARI_DIR_B}/tp-base.sorted.vcf.gz
tabix ${TRUVARI_DIR_B}/tp-base.sorted.vcf.gz

#Ensure parent directories set up before Truvari execution
mkdir -p $OUTPUT_DIR/Call
mkdir -p $OUTPUT_DIR/Base

#Truvari creates the output directory during execution and won't overwrite an existing directory. Remove target $OUTPUT_DIR if it already exists.
if [ -d $OUTPUT_DIR/Call/FromTPCall ]
then
	echo "$OUTPUT_DIR already exists! Removing to allow truvari to run!.. "
	rm -r $OUTPUT_DIR/Call/FromTPCall
fi

if [ -d $OUTPUT_DIR/Call/FromTPBase ]
then
        echo "$OUTPUT_DIR already exists! Removing to allow truvari to run!.. "
        rm -r $OUTPUT_DIR/Call/FromTPBase
fi

if [ -d $OUTPUT_DIR/Base/FromTPCall ]
then
        echo "$OUTPUT_DIR already exists! Removing to allow truvari to run!.. "
        rm -r $OUTPUT_DIR/Base/FromTPCall
fi

if [ -d $OUTPUT_DIR/Base/FromTPBase ]
then
        echo "$OUTPUT_DIR already exists! Removing to allow truvari to run!.. "
        rm -r $OUTPUT_DIR/Base/FromTPBase
fi

#Execute Truvari Bench to compare the VCF files provided in the script's arguments
truvari bench --typeignore -o $OUTPUT_DIR/Call/FromTPCall -f $REF_GENOME -b ${TRUVARI_DIR_A}/tp-call.sorted.vcf.gz -c ${TRUVARI_DIR_B}/tp-call.sorted.vcf.gz -s $MIN_SIZE --sizemax $MAX_SIZE -r $MAX_REF_DIST -p 0 -P $OVERLAP -C $MAX_REF_DIST
truvari bench --typeignore -o $OUTPUT_DIR/Call/FromTPBase -f $REF_GENOME -b ${TRUVARI_DIR_A}/tp-call.sorted.vcf.gz -c ${TRUVARI_DIR_B}/tp-base.sorted.vcf.gz -s $MIN_SIZE --sizemax $MAX_SIZE -r $MAX_REF_DIST -p 0 -P $OVERLAP -C $MAX_REF_DIST
truvari bench --typeignore -o $OUTPUT_DIR/Base/FromTPCall -f $REF_GENOME -b ${TRUVARI_DIR_A}/tp-base.sorted.vcf.gz -c ${TRUVARI_DIR_B}/tp-call.sorted.vcf.gz -s $MIN_SIZE --sizemax $MAX_SIZE -r $MAX_REF_DIST -p 0 -P $OVERLAP -C $MAX_REF_DIST
Shell BCFtools tabix From line 3 of Scripts/compare_sv_files_w_truvari_ignore_type_quads.sh 
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SV_FILE_A=$1
TRUVARI_DIR=$2
REF_GENOME=$3
MIN_SIZE=$4
MAX_SIZE=$5
OVERLAP=$6
MAX_REF_DIST=$7
OUTPUT_DIR=$8

#Truvari requires sorted, zipped, and indexed VCF files as input. (Re)Generate files before starting Truvari bench
bcftools sort -o ${SV_FILE_A}.sorted $SV_FILE_A
bgzip -c ${SV_FILE_A}.sorted > ${SV_FILE_A}.gz
tabix ${SV_FILE_A}.gz

bcftools sort -o ${TRUVARI_DIR}/tp-call.sorted.vcf $TRUVARI_DIR/tp-call.vcf
bgzip -c ${TRUVARI_DIR}/tp-call.sorted.vcf > ${TRUVARI_DIR}/tp-call.sorted.vcf.gz
tabix ${TRUVARI_DIR}/tp-call.sorted.vcf.gz

bcftools sort -o ${TRUVARI_DIR}/tp-base.sorted.vcf $TRUVARI_DIR/tp-base.vcf
bgzip -c ${TRUVARI_DIR}/tp-base.sorted.vcf > ${TRUVARI_DIR}/tp-base.sorted.vcf.gz
tabix ${TRUVARI_DIR}/tp-base.sorted.vcf.gz

#Ensure parent directories set up before Truvari execution
mkdir -p $OUTPUT_DIR

#Truvari creates the output directory during execution and won't overwrite an existing directory. Remove target $OUTPUT_DIR if it already exists.
if [ -d $OUTPUT_DIR/FromTPCall ]
then
	echo "$OUTPUT_DIR already exists! Removing to allow truvari to run!.. "
	rm -r $OUTPUT_DIR/FromTPCall
fi

if [ -d $OUTPUT_DIR/FromTPBase ]
then
        echo "$OUTPUT_DIR already exists! Removing to allow truvari to run!.. "
        rm -r $OUTPUT_DIR/FromTPBase
fi

#Execute Truvari Bench to compare the VCF files provided in the script's arguments
truvari bench --typeignore -o $OUTPUT_DIR/FromTPCall -f $REF_GENOME -b ${SV_FILE_A}.gz -c ${TRUVARI_DIR}/tp-call.sorted.vcf.gz -s $MIN_SIZE --sizemax $MAX_SIZE -r $MAX_REF_DIST -p 0 -P $OVERLAP -C $MAX_REF_DIST
truvari bench --typeignore -o $OUTPUT_DIR/FromTPBase -f $REF_GENOME -b ${SV_FILE_A}.gz -c ${TRUVARI_DIR}/tp-base.sorted.vcf.gz -s $MIN_SIZE --sizemax $MAX_SIZE -r $MAX_REF_DIST -p 0 -P $OVERLAP -C $MAX_REF_DIST
Shell BCFtools tabix From line 3 of Scripts/compare_sv_files_w_truvari_ignore_type_trips.sh 
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SV_FILE_A=$1
SV_FILE_B=$2
REF_GENOME=$3
MIN_SIZE=$4
MAX_SIZE=$5
OVERLAP=$6
MAX_REF_DIST=$7
OUTPUT_DIR=$8

#Truvari requires sorted, zipped, and indexed VCF files as input. (Re)Generate files before starting Truvari bench
bcftools sort -o ${SV_FILE_A}.sorted $SV_FILE_A
bgzip -c ${SV_FILE_A}.sorted > ${SV_FILE_A}.gz
tabix ${SV_FILE_A}.gz

bcftools sort -o ${SV_FILE_B}.sorted $SV_FILE_B
bgzip -c ${SV_FILE_B}.sorted > ${SV_FILE_B}.gz
tabix ${SV_FILE_B}.gz

#Ensure parent directories set up before Truvari execution
mkdir -p $OUTPUT_DIR

#Truvari creates the output directory during execution and won't overwrite an existing directory. Remove target $OUTPUT_DIR if it already exists.
if [ -d $OUTPUT_DIR ]
then
	echo "$OUTPUT_DIR already exists! Removing to allow truvari to run!.. "
	rm -r $OUTPUT_DIR
fi

#Execute Truvari Bench to compare the VCF files provided in the script's arguments
truvari bench -o $OUTPUT_DIR -f $REF_GENOME -b ${SV_FILE_A}.gz -c ${SV_FILE_B}.gz -s $MIN_SIZE --sizemax $MAX_SIZE -r $MAX_REF_DIST -p 0 -P $OVERLAP -C $MAX_REF_DIST
Shell BCFtools tabix From line 3 of Scripts/compare_sv_files_w_truvari_pairs.sh 
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TRUVARI_DIR_A=$1
TRUVARI_DIR_B=$2
REF_GENOME=$3
MIN_SIZE=$4
MAX_SIZE=$5
OVERLAP=$6
MAX_REF_DIST=$7
OUTPUT_DIR=$8

#Truvari requires sorted, zipped, and indexed VCF files as input. (Re)Generate files before starting Truvari bench
bcftools sort -o ${TRUVARI_DIR_A}/tp-call.sorted.vcf $TRUVARI_DIR_A/tp-call.vcf
bgzip -c ${TRUVARI_DIR_A}/tp-call.sorted.vcf > ${TRUVARI_DIR_A}/tp-call.sorted.vcf.gz
tabix ${TRUVARI_DIR_A}/tp-call.sorted.vcf.gz

bcftools sort -o ${TRUVARI_DIR_A}/tp-base.sorted.vcf $TRUVARI_DIR_A/tp-base.vcf
bgzip -c ${TRUVARI_DIR_A}/tp-base.sorted.vcf > ${TRUVARI_DIR_A}/tp-base.sorted.vcf.gz
tabix ${TRUVARI_DIR_A}/tp-base.sorted.vcf.gz

bcftools sort -o ${TRUVARI_DIR_B}/tp-call.sorted.vcf $TRUVARI_DIR_B/tp-call.vcf
bgzip -c ${TRUVARI_DIR_B}/tp-call.sorted.vcf > ${TRUVARI_DIR_B}/tp-call.sorted.vcf.gz
tabix ${TRUVARI_DIR_B}/tp-call.sorted.vcf.gz

bcftools sort -o ${TRUVARI_DIR_B}/tp-base.sorted.vcf $TRUVARI_DIR_B/tp-base.vcf
bgzip -c ${TRUVARI_DIR_B}/tp-base.sorted.vcf > ${TRUVARI_DIR_B}/tp-base.sorted.vcf.gz
tabix ${TRUVARI_DIR_B}/tp-base.sorted.vcf.gz

#Ensure parent directories set up before Truvari execution
mkdir -p $OUTPUT_DIR/Call
mkdir -p $OUTPUT_DIR/Base

#Truvari creates the output directory during execution and won't overwrite an existing directory. Remove target $OUTPUT_DIR if it already exists.
if [ -d $OUTPUT_DIR/Call/FromTPCall ]
then
	echo "$OUTPUT_DIR already exists! Removing to allow truvari to run!.. "
	rm -r $OUTPUT_DIR/Call/FromTPCall
fi

if [ -d $OUTPUT_DIR/Call/FromTPBase ]
then
        echo "$OUTPUT_DIR already exists! Removing to allow truvari to run!.. "
        rm -r $OUTPUT_DIR/Call/FromTPBase
fi

if [ -d $OUTPUT_DIR/Base/FromTPCall ]
then
        echo "$OUTPUT_DIR already exists! Removing to allow truvari to run!.. "
        rm -r $OUTPUT_DIR/Base/FromTPCall
fi

if [ -d $OUTPUT_DIR/Base/FromTPBase ]
then
        echo "$OUTPUT_DIR already exists! Removing to allow truvari to run!.. "
        rm -r $OUTPUT_DIR/Base/FromTPBase
fi

#Execute Truvari Bench to compare the VCF files provided in the script's arguments
truvari bench -o $OUTPUT_DIR/Call/FromTPCall -f $REF_GENOME -b ${TRUVARI_DIR_A}/tp-call.sorted.vcf.gz -c ${TRUVARI_DIR_B}/tp-call.sorted.vcf.gz -s $MIN_SIZE --sizemax $MAX_SIZE -r $MAX_REF_DIST -p 0 -P $OVERLAP -C $MAX_REF_DIST
truvari bench -o $OUTPUT_DIR/Call/FromTPBase -f $REF_GENOME -b ${TRUVARI_DIR_A}/tp-call.sorted.vcf.gz -c ${TRUVARI_DIR_B}/tp-base.sorted.vcf.gz -s $MIN_SIZE --sizemax $MAX_SIZE -r $MAX_REF_DIST -p 0 -P $OVERLAP -C $MAX_REF_DIST
truvari bench -o $OUTPUT_DIR/Base/FromTPCall -f $REF_GENOME -b ${TRUVARI_DIR_A}/tp-base.sorted.vcf.gz -c ${TRUVARI_DIR_B}/tp-call.sorted.vcf.gz -s $MIN_SIZE --sizemax $MAX_SIZE -r $MAX_REF_DIST -p 0 -P $OVERLAP -C $MAX_REF_DIST
Shell BCFtools tabix From line 3 of Scripts/compare_sv_files_w_truvari_quads.sh 
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SV_FILE_A=$1
TRUVARI_DIR=$2
REF_GENOME=$3
MIN_SIZE=$4
MAX_SIZE=$5
OVERLAP=$6
MAX_REF_DIST=$7
OUTPUT_DIR=$8

#Truvari requires sorted, zipped, and indexed VCF files as input. (Re)Generate files before starting Truvari bench
bcftools sort -o ${SV_FILE_A}.sorted $SV_FILE_A
bgzip -c ${SV_FILE_A}.sorted > ${SV_FILE_A}.gz
tabix ${SV_FILE_A}.gz

bcftools sort -o ${TRUVARI_DIR}/tp-call.sorted.vcf $TRUVARI_DIR/tp-call.vcf
bgzip -c ${TRUVARI_DIR}/tp-call.sorted.vcf > ${TRUVARI_DIR}/tp-call.sorted.vcf.gz
tabix ${TRUVARI_DIR}/tp-call.sorted.vcf.gz

bcftools sort -o ${TRUVARI_DIR}/tp-base.sorted.vcf $TRUVARI_DIR/tp-base.vcf
bgzip -c ${TRUVARI_DIR}/tp-base.sorted.vcf > ${TRUVARI_DIR}/tp-base.sorted.vcf.gz
tabix ${TRUVARI_DIR}/tp-base.sorted.vcf.gz

#Ensure parent directories set up before Truvari execution
mkdir -p $OUTPUT_DIR

#Truvari creates the output directory during execution and won't overwrite an existing directory. Remove target $OUTPUT_DIR if it already exists.
if [ -d $OUTPUT_DIR/FromTPCall ]
then
	echo "$OUTPUT_DIR already exists! Removing to allow truvari to run!.. "
	rm -r $OUTPUT_DIR/FromTPCall
fi

if [ -d $OUTPUT_DIR/FromTPBase ]
then
        echo "$OUTPUT_DIR already exists! Removing to allow truvari to run!.. "
        rm -r $OUTPUT_DIR/FromTPBase
fi

#Execute Truvari Bench to compare the VCF files provided in the script's arguments
truvari bench -o $OUTPUT_DIR/FromTPCall -f $REF_GENOME -b ${SV_FILE_A}.gz -c ${TRUVARI_DIR}/tp-call.sorted.vcf.gz -s $MIN_SIZE --sizemax $MAX_SIZE -r $MAX_REF_DIST -p 0 -P $OVERLAP -C $MAX_REF_DIST
truvari bench -o $OUTPUT_DIR/FromTPBase -f $REF_GENOME -b ${SV_FILE_A}.gz -c ${TRUVARI_DIR}/tp-base.sorted.vcf.gz -s $MIN_SIZE --sizemax $MAX_SIZE -r $MAX_REF_DIST -p 0 -P $OVERLAP -C $MAX_REF_DIST
Shell BCFtools tabix From line 3 of Scripts/compare_sv_files_w_truvari_trips.sh 
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THREADS=$1
READS_DIR=$2
READ_FILES_LIST=$3

echo "Reformatting SRA Files for all Accessions detailed in $READ_FILES_LIST to FASTQ..."
mkdir -p $READS_DIR

readarray ACCESSIONS_ARRAY < $READ_FILES_LIST
for ACCESSION in "${ACCESSIONS_ARRAY[@]}"
do
	STRIP_ACCESSION=$(echo $ACCESSION | tr -d "\n")
	#fasterq-dump --threads $THREADS -O $READS_DIR ${READS_DIR}/${STRIP_ACCESSION}.sra
        if [[ ! -f "${READS_DIR}/${STRIP_ACCESSION}.fastq" ]]; then
		fastq-dump -O $READS_DIR ${READS_DIR}/${STRIP_ACCESSION}.sra
        else
                echo "${READS_DIR}/${STRIP_ACCESSION}.fastq already Exists! Skipping fastq-dump..."
	fi
	#fastq-dump -O $READS_DIR ${READS_DIR}/${STRIP_ACCESSION}.sra
done

echo "Reformatting complete!.."
Shell From line 3 of Scripts/fasterq_dump_read_files.sh 
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GENOME_FILE=$1
REGIONS_LIST=$2
OUTPUT_FILE=$3

#Check for an index of the reference file and create it if it does not exist
if [ ! -f ${GENOME_FASTA}.fai ]
then
	echo "Creating index for $GENOME_FILE..."
	samtools faidx $GENOME_FILE
fi

#Extract regions of interest based on contents of the CHROM_LIST_FILE path provided
echo "Extracting regions specified in $REGIONS_LIST..."
samtools faidx $GENOME_FILE -r $REGIONS_LIST > $OUTPUT_FILE
bgzip -c $OUTPUT_FILE > $OUTPUT_FILE.gz
samtools faidx $OUTPUT_FILE.gz
Shell SAMtools From line 3 of Scripts/filter_genome_fasta.sh 
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READS_DIR=$1
FILE_MAX=$2
READ_FILES_LIST=$3

echo "Starting prefetching of all Accessions detailed in $READ_FILES_LIST..."
mkdir -p $READS_DIR

readarray ACCESSIONS_ARRAY < $READ_FILES_LIST
for ACCESSION in "${ACCESSIONS_ARRAY[@]}"
do
	STRIP_ACCESSION=$(echo $ACCESSION | tr -d "\n")
	if [[ ! -f "${READS_DIR}/${STRIP_ACCESSION}.sra" ]]; then
    		prefetch --max-size $FILE_MAX -o ${READS_DIR}/${STRIP_ACCESSION}.sra ${STRIP_ACCESSION}
	else
		echo "${READS_DIR}/${STRIP_ACCESSION}.sra already Exists! Skipping prefetch..."
	fi
	#prefetch --max-size $FILE_MAX -o ${READS_DIR}/${STRIP_ACCESSION}.sra ${STRIP_ACCESSION}
done

echo "Prefetching complete!.."
Shell From line 3 of Scripts/prefetch_read_files_list.sh 
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CORES=$1
ANALYSIS_DIR=$2
REF_GENOME=$3
QRY_GENOME=$4
QRY_ID=$5
WORKING_DIR=`pwd` # Stores pipeline's working directory to allow for return


#PAV Snakemake operates on zipped ref genome file, verify it exists before proceeding
if [ ! -f ${REF_GENOME}.gz ]
then
	echo "Zipping and indexing $REF_GENOME as PAV setup!.."
	bgzip -c $REF_GENOME > ${REF_GENOME}.gz
	faidx ${REF_GENOME}.gz
fi

#Build config.json for PAV based on inputs
REF_ABS_PATH=`echo "$(cd "$(dirname "$REF_GENOME")"; pwd)/$(basename "$REF_GENOME")"` #Convert Relative to Abs path for PAV Config
echo "{" > $ANALYSIS_DIR/config.json; echo "	\"reference\": \"${REF_ABS_PATH}.gz\"" >> $ANALYSIS_DIR/config.json; echo "}" >> $ANALYSIS_DIR/config.json

#Add required query information file to PAV before starting execution
QRY_ABS_PATH=`echo "$(cd "$(dirname "$QRY_GENOME")"; pwd)/$(basename "$QRY_GENOME")"` #Convert Relative to Abs path for PAV Config
echo "NAME	HAP1	HAP2" > $ANALYSIS_DIR/assemblies.tsv
echo "$QRY_ID	$QRY_ABS_PATH" >> $ANALYSIS_DIR/assemblies.tsv

#Change to PAV working directory before starting per instruction on PAV repo
echo "Changing directory to $ANALYSIS_DIR and starting PAV's SnakeMake pipeline!.."
cd $ANALYSIS_DIR

#Check if runlocal in ANALYSIS_DIR is successfully linked to run local in $PAV and link if not
if [ ! -e ./runlocal ]
then
	ln -s $PAV/runlocal ./
fi

#Run PAV
./runlocal $CORES

#Return to SV-JIM Working directory
echo "Pipeline complete! Returning to $WORKING_DIR!.."
cd $WORKING_DIR
Shell From line 3 of Scripts/run-PAV-SnakeMake-pipe.sh 
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ALL_SV_FILE=$1
SV_FILE_PREFIX=$2

# Segment only those SV types identifiable by PAV based on their SVTYPE field found in the VCF output
bcftools filter -i 'SVTYPE == "DEL"' -o ${SV_FILE_PREFIX}.DEL.vcf $ALL_SV_FILE
bcftools filter -i 'SVTYPE == "INS"' -o ${SV_FILE_PREFIX}.INS.vcf $ALL_SV_FILE
bcftools filter -i 'SVTYPE == "INV"' -o ${SV_FILE_PREFIX}.INV.vcf $ALL_SV_FILE

#Segment SV types by size thresholds
for TYPE in DEL INS INV
do
	bcftools filter -e 'INFO/SVLEN > 100 || INFO/SVLEN < -100' -o ${SV_FILE_PREFIX}.${TYPE}.SSm.vcf ${SV_FILE_PREFIX}.${TYPE}.vcf
	bcftools filter -i '(INFO/SVLEN > 100 && INFO/SVLEN <= 1000) || (INFO/SVLEN < -100 && INFO/SVLEN >= -1000)' -o ${SV_FILE_PREFIX}.${TYPE}.Sml.vcf ${SV_FILE_PREFIX}.${TYPE}.vcf
	bcftools filter -i '(INFO/SVLEN > 1000 && INFO/SVLEN <= 100000) || (INFO/SVLEN < -1000 && INFO/SVLEN >= -100000)' -o ${SV_FILE_PREFIX}.${TYPE}.Med.vcf ${SV_FILE_PREFIX}.${TYPE}.vcf
	bcftools filter -i 'INFO/SVLEN > 100000 || INFO/SVLEN < -100000' -o ${SV_FILE_PREFIX}.${TYPE}.Lrg.vcf ${SV_FILE_PREFIX}.${TYPE}.vcf
done
Shell BCFtools From line 3 of Scripts/segment_pav_w_bcftools.sh 
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ALL_SV_FILE=$1
SV_FILE_PREFIX=$2
TOOL_NAME=$3

# Segment VCF files by type for all types based on the values found in the SVTYPE field of each  VCF output
bcftools filter -i 'SVTYPE == "DEL"' -o ${SV_FILE_PREFIX}.DEL.vcf $ALL_SV_FILE
bcftools filter -i 'SVTYPE == "INS"' -o ${SV_FILE_PREFIX}.INS.vcf $ALL_SV_FILE
bcftools filter -i 'SVTYPE == "DUP" || SVTYPE == "DUP:INT" || SVTYPE == "DUP:TANDEM"' -o ${SV_FILE_PREFIX}.DUP.vcf $ALL_SV_FILE
bcftools filter -i 'SVTYPE == "INV"' -o ${SV_FILE_PREFIX}.INV.vcf $ALL_SV_FILE
bcftools filter -i 'SVTYPE == "BND"' -o ${SV_FILE_PREFIX}.BND.vcf $ALL_SV_FILE

#Segment SV types by size thresholds
for TYPE in DEL INS DUP
do
        bcftools filter -e 'INFO/SVLEN > 100 || INFO/SVLEN < -100' -o ${SV_FILE_PREFIX}.${TYPE}.SSm.vcf ${SV_FILE_PREFIX}.${TYPE}.vcf
        bcftools filter -i '(INFO/SVLEN > 100 && INFO/SVLEN <= 1000) || (INFO/SVLEN < -100 && INFO/SVLEN >= -1000)' -o ${SV_FILE_PREFIX}.${TYPE}.Sml.vcf ${SV_FILE_PREFIX}.${TYPE}.vcf
        bcftools filter -i '(INFO/SVLEN > 1000 && INFO/SVLEN <= 100000) || (INFO/SVLEN < -1000 && INFO/SVLEN >= -100000)' -o ${SV_FILE_PREFIX}.${TYPE}.Med.vcf ${SV_FILE_PREFIX}.${TYPE}.vcf
        bcftools filter -i 'INFO/SVLEN > 100000 || INFO/SVLEN < -100000' -o ${SV_FILE_PREFIX}.${TYPE}.Lrg.vcf ${SV_FILE_PREFIX}.${TYPE}.vcf
done

if [ "SVIM" = $TOOL_NAME ] || [ "SVIM-ASM" = $TOOL_NAME ]; then
	bcftools filter -e '(POS-INFO/END) > 100 || (POS-INFO/END) < -100' -o ${SV_FILE_PREFIX}.INV.SSm.vcf ${SV_FILE_PREFIX}.INV.vcf
	bcftools filter -i '((POS-INFO/END) > 100 && (POS-INFO/END) <= 1000) || ((POS-INFO/END) < -100 && (POS-INFO/END) >= -1000)' -o ${SV_FILE_PREFIX}.INV.Sml.vcf ${SV_FILE_PREFIX}.INV.vcf
	bcftools filter -i '((POS-INFO/END) > 1000 && (POS-INFO/END) <= 100000) || ((POS-INFO/END) < -1000 && (POS-INFO/END) >= -100000)' -o ${SV_FILE_PREFIX}.INV.Med.vcf ${SV_FILE_PREFIX}.INV.vcf
	bcftools filter -i '(POS-INFO/END) > 100000 || (POS-INFO/END) < -100000' -o ${SV_FILE_PREFIX}.INV.Lrg.vcf ${SV_FILE_PREFIX}.INV.vcf
else
        bcftools filter -e 'INFO/SVLEN > 100 || INFO/SVLEN < -100' -o ${SV_FILE_PREFIX}.INV.SSm.vcf ${SV_FILE_PREFIX}.INV.vcf
        bcftools filter -i '(INFO/SVLEN > 100 && INFO/SVLEN <= 1000) || (INFO/SVLEN < -100 && INFO/SVLEN >= -1000)' -o ${SV_FILE_PREFIX}.INV.Sml.vcf ${SV_FILE_PREFIX}.INV.vcf
        bcftools filter -i '(INFO/SVLEN > 1000 && INFO/SVLEN <= 100000) || (INFO/SVLEN < -1000 && INFO/SVLEN >= -100000)' -o ${SV_FILE_PREFIX}.INV.Med.vcf ${SV_FILE_PREFIX}.INV.vcf
        bcftools filter -i 'INFO/SVLEN > 100000 || INFO/SVLEN < -100000' -o ${SV_FILE_PREFIX}.INV.Lrg.vcf ${SV_FILE_PREFIX}.INV.vcf
fi
Shell BCFtools From line 3 of Scripts/segment_sv_types_w_bcftools.sh 
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WRITE_MODE=$1
SV_TYPE=$2
OUTPUT_FILE=$3

#If first to write, create header
if [ "W" = $WRITE_MODE ] || [ "w" = $WRITE_MODE ]; then
        echo "TYPE      SSM     SML     MED     LRG     TOTAL" > $OUTPUT_FILE
fi

#Grab guaranteed variables (With BND there will be less since BNDs don't come in multiple sizes)
SV_TYPE=$2
OUTPUT_FILE=$3

ALL_VCF=$4
TOTAL_COUNT=$(grep -v "^#" $ALL_VCF | grep -c "$SV_TYPE")

#If the SV_TYPE is BND write the row accordingly with only one total calculated (rest 0s)
if [ "BND" = $SV_TYPE ]; then
	echo "$SV_TYPE	$TOTAL_COUNT	0	0	0	$TOTAL_COUNT" >> $OUTPUT_FILE
else #Otherwise calculate all sizes and write each entry to file
	SSM_VCF=$5
        SSM_COUNT=$(grep -vc "^#" $SSM_VCF)

	SML_VCF=$6
        SML_COUNT=$(grep -vc "^#" $SML_VCF)

	MED_VCF=$7
        MED_COUNT=$(grep -vc "^#" $MED_VCF)

	LRG_VCF=$8
        LRG_COUNT=$(grep -vc "^#" $LRG_VCF)

	echo "$SV_TYPE	$SSM_COUNT	$SML_COUNT	$MED_COUNT	$LRG_COUNT	$TOTAL_COUNT" >> $OUTPUT_FILE
fi
Shell From line 4 of Scripts/summarize_SV_counts.sh 
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OUTPUT_FILE=$1
SSM_FILE=$2
SML_FILE=$3
MED_FILE=$4
LRG_FILE=$5
TOTAL_FILE=$6

#Extract intersection size column from files into array (Ordered as: Header,#DEL,#INS,#DUP,#INV,#BND,#TOTAL)
SSM_ARRAY=($(awk '{ print $11 }' $SSM_FILE))
SML_ARRAY=($(awk '{ print $11 }' $SML_FILE))
MED_ARRAY=($(awk '{ print $11 }' $MED_FILE))
LRG_ARRAY=($(awk '{ print $11 }' $LRG_FILE))
TOTAL_ARRAY=($(awk '{ print $11 }' $TOTAL_FILE))

#Create file by adding headers
echo "TYPE	SSM	SML	MED	LRG	TOTAL" > $OUTPUT_FILE

#Add DEL counts to file
SSM_DEL_COUNT="${SSM_ARRAY[1]}"
SML_DEL_COUNT="${SML_ARRAY[1]}"
MED_DEL_COUNT="${MED_ARRAY[1]}"
LRG_DEL_COUNT="${LRG_ARRAY[1]}"
TOTAL_DEL_COUNT="${TOTAL_ARRAY[1]}"
echo "DEL	$SSM_DEL_COUNT	$SML_DEL_COUNT	$MED_DEL_COUNT	$LRG_DEL_COUNT	$TOTAL_DEL_COUNT" >> $OUTPUT_FILE

#Add INS counts to file
SSM_INS_COUNT="${SSM_ARRAY[2]}"
SML_INS_COUNT="${SML_ARRAY[2]}"
MED_INS_COUNT="${MED_ARRAY[2]}"
LRG_INS_COUNT="${LRG_ARRAY[2]}"
TOTAL_INS_COUNT="${TOTAL_ARRAY[2]}"
echo "INS	$SSM_INS_COUNT	$SML_INS_COUNT	$MED_INS_COUNT	$LRG_INS_COUNT	$TOTAL_INS_COUNT" >> $OUTPUT_FILE

#Add DUP counts to file
SSM_DUP_COUNT="${SSM_ARRAY[3]}"
SML_DUP_COUNT="${SML_ARRAY[3]}"
MED_DUP_COUNT="${MED_ARRAY[3]}"
LRG_DUP_COUNT="${LRG_ARRAY[3]}"
TOTAL_DUP_COUNT="${TOTAL_ARRAY[3]}"
echo "DUP	$SSM_DUP_COUNT	$SML_DUP_COUNT	$MED_DUP_COUNT	$LRG_DUP_COUNT	$TOTAL_DUP_COUNT" >> $OUTPUT_FILE

#Add INV counts to file
SSM_INV_COUNT="${SSM_ARRAY[4]}"
SML_INV_COUNT="${SML_ARRAY[4]}"
MED_INV_COUNT="${MED_ARRAY[4]}"
LRG_INV_COUNT="${LRG_ARRAY[4]}"
TOTAL_INV_COUNT="${TOTAL_ARRAY[4]}"
echo "INV	$SSM_INV_COUNT	$SML_INV_COUNT	$MED_INV_COUNT	$LRG_INV_COUNT	$TOTAL_INV_COUNT" >> $OUTPUT_FILE

#Add BND counts to file
SSM_BND_COUNT="${SSM_ARRAY[5]}"
echo "BND	$SSM_BND_COUNT	0	0	0	$SSM_BND_COUNT" >> $OUTPUT_FILE

#Add Totals counts to file
SSM_TOTAL_COUNT="${SSM_ARRAY[6]}"
SML_TOTAL_COUNT="${SML_ARRAY[5]}" # One less row in sml files since they dont contain breakpoints of size 1
MED_TOTAL_COUNT="${MED_ARRAY[5]}" # One less row in med files since they dont contain breakpoints of size 1
LRG_TOTAL_COUNT="${LRG_ARRAY[5]}" # One less row in lrg files since they dont contain breakpoints of size 1
TOTAL_TOTAL_COUNT="${TOTAL_ARRAY[6]}"
echo "ALL	$SSM_TOTAL_COUNT	$SML_TOTAL_COUNT	$MED_TOTAL_COUNT	$LRG_TOTAL_COUNT	$TOTAL_TOTAL_COUNT" >> $OUTPUT_FILE
Shell From line 3 of Scripts/total_intersection_no_pav_counts.sh 
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OUTPUT_FILE=$1
SSM_FILE=$2
SML_FILE=$3
MED_FILE=$4
LRG_FILE=$5
TOTAL_FILE=$6

#Extract intersection size column from files into array (Ordered as: Header,#DEL,#INS,#INV,#TOTAL)
SSM_ARRAY=($(awk '{ print $11 }' $SSM_FILE))
SML_ARRAY=($(awk '{ print $11 }' $SML_FILE))
MED_ARRAY=($(awk '{ print $11 }' $MED_FILE))
LRG_ARRAY=($(awk '{ print $11 }' $LRG_FILE))
TOTAL_ARRAY=($(awk '{ print $11 }' $TOTAL_FILE))

#Create file by adding headers
echo "TYPE	SSM	SML	MED	LRG	TOTAL" > $OUTPUT_FILE

#Add DEL counts to file
SSM_DEL_COUNT="${SSM_ARRAY[1]}"
SML_DEL_COUNT="${SML_ARRAY[1]}"
MED_DEL_COUNT="${MED_ARRAY[1]}"
LRG_DEL_COUNT="${LRG_ARRAY[1]}"
TOTAL_DEL_COUNT="${TOTAL_ARRAY[1]}"
echo "DEL	$SSM_DEL_COUNT	$SML_DEL_COUNT	$MED_DEL_COUNT	$LRG_DEL_COUNT	$TOTAL_DEL_COUNT" >> $OUTPUT_FILE

#Add INS counts to file
SSM_INS_COUNT="${SSM_ARRAY[2]}"
SML_INS_COUNT="${SML_ARRAY[2]}"
MED_INS_COUNT="${MED_ARRAY[2]}"
LRG_INS_COUNT="${LRG_ARRAY[2]}"
TOTAL_INS_COUNT="${TOTAL_ARRAY[2]}"
echo "INS	$SSM_INS_COUNT	$SML_INS_COUNT	$MED_INS_COUNT	$LRG_INS_COUNT	$TOTAL_INS_COUNT" >> $OUTPUT_FILE

#Add INV counts to file
SSM_INV_COUNT="${SSM_ARRAY[3]}"
SML_INV_COUNT="${SML_ARRAY[3]}"
MED_INV_COUNT="${MED_ARRAY[3]}"
LRG_INV_COUNT="${LRG_ARRAY[3]}"
TOTAL_INV_COUNT="${TOTAL_ARRAY[3]}"
echo "INV	$SSM_INV_COUNT	$SML_INV_COUNT	$MED_INV_COUNT	$LRG_INV_COUNT	$TOTAL_INV_COUNT" >> $OUTPUT_FILE

#Add Totals counts to file
SSM_TOTAL_COUNT="${SSM_ARRAY[4]}"
SML_TOTAL_COUNT="${SML_ARRAY[4]}"
MED_TOTAL_COUNT="${MED_ARRAY[4]}"
LRG_TOTAL_COUNT="${LRG_ARRAY[4]}"
TOTAL_TOTAL_COUNT="${TOTAL_ARRAY[4]}"
echo "ALL	$SSM_TOTAL_COUNT	$SML_TOTAL_COUNT	$MED_TOTAL_COUNT	$LRG_TOTAL_COUNT	$TOTAL_TOTAL_COUNT" >> $OUTPUT_FILE
Shell From line 3 of Scripts/total_intersection_with_pav_counts.sh 
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INPUT_FILE=$1

SSM_COUNT=$(awk '{sum+=$2;} END{print sum;}' $INPUT_FILE)
SML_COUNT=$(awk '{sum+=$3;} END{print sum;}' $INPUT_FILE)
MED_COUNT=$(awk '{sum+=$4;} END{print sum;}' $INPUT_FILE)
LRG_COUNT=$(awk '{sum+=$5;} END{print sum;}' $INPUT_FILE)
TOTAL_COUNT=$(awk '{sum+=$6;} END{print sum;}' $INPUT_FILE)

echo "ALL	$SSM_COUNT	$SML_COUNT	$MED_COUNT	$LRG_COUNT	$TOTAL_COUNT" >> $INPUT_FILE
Shell From line 3 of Scripts/total_SV_counts.sh
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Free

Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/CMalcolmTodd/SV-JIM
Name: sv-jim
Version: 1
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Copyright: Public Domain
License: MIT License
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