Snakemake module containing different analyses provided by parabricks.

public 1yr ago Version: v1.1.0 0 bookmarks

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Snakemake module containing an array of steps provided by the parabricks tookit

:speech_balloon: Introduction

The module contains rules to align .fastq -files and call variants in the resulting .bam -files using Clara Parabricks . To use this module a server with access to one or more compatible NVIDIA GPUs is required. Input data should be trimmed .fastq -files and we recommend to generate these with hydra-genetics/prealignment for a smooth transition. In order to make use of read group information, add machine, flowcell and library specifics to units.tsv .

:heavy_exclamation_mark: Dependencies

In order to use this module, the following dependencies are required:

:school_satchel: Preparations

Sample and unit data

Input data should be added to samples.tsv and units.tsv . The following information need to be added to these files:

Column Id	Description
`samples.tsv`
sample	unique sample/patient id, one per row
tumor_content	ratio of tumor cells to total cells
`units.tsv`
sample	same sample/patient id as in `samples.tsv`
type	data type identifier (one letter), can be one of T umor, N ormal, R NA
platform	type of sequencing platform, e.g. `NovaSeq`
machine	specific machine id, e.g. NovaSeq instruments have `@Axxxxx`
flowcell	identifer of flowcell used
lane	flowcell lane number
barcode	sequence library barcode/index, connect forward and reverse indices by `+` , e.g. `ATGC+ATGC`
fastq1/2	absolute path to forward and reverse reads
adapter	adapter sequences to be trimmed, separated by comma

Reference data

Reference files should be specified in config.yaml in the section reference . A .fasta -file is needed as well as a .vcf file containing known indels used during the alignment process. For the RNA alignment part, genome_dir should specify a directory containing reference files generated by STAR .

:rocket: Usage

To use this module in your workflow, follow the description in the snakemake docs . Add the module to your Snakefile like so:

module parabricks:
 snakefile:
 github(
 "hydra-genetics/parabricks",
 path="workflow/Snakefile",
 tag="1.0.0",
 )
 config:
 config
use rule * from parabricks as parabricks_*

Compatibility

Latest:

prealignment:v1.1.0

See COMPATIBLITY.md file for a complete list of module compatibility.

Output files

The following output files should be targeted via another rule:

File	Description
`parabricks/pbrun_deepvariant/{sample}.vcf`	variant call file generated by deepvariant
`parabricks/pbrun_fq2bam/{sample}_{type}.bam`	alignment file generated by BWA-mem
`parabricks/pbrun_mutectcaller_t/{sample}_T.vcf`	variant call file generated by Mutect2 using tumor-only mode
`parabricks/pbrun_mutectcaller_tn/{sample}.vcf`	variant call file generated by Mutect2 using tumor/normal mode
`parabricks/pbrun_rna_fq2bam/{sample}_R.bam`	alignment file generated by STAR

:judge: Rule Graph

rule_graph

Code Snippets

shell:
    "{params.cuda} pbrun deepvariant "
    "--ref {input.fasta} "
    "--in-bam {input.bam} "
    "--num-gpus {params.num_gpus} "
    "--out-variants {output.vcf} "
    "{params.extra} "
    "--tmp-dir parabricks/pbrun_deepvariant/{wildcards.sample} &> {log}"

SnakeMake DeepVariant From line 39 of rules/pbrun.smk

shell:
    "{params.cuda} pbrun fq2bam "
    "--ref {input.fasta} "
    "--in-fq {params.in_fq} "
    "--knownSites {input.sites} "
    "--num-gpus {params.num_gpus} "
    "--out-bam {output.bam} "
    "--out-duplicate-metrics {output.metrics} "
    "--out-recal-file {output.recal} "
    "{params.extra} "
    "--tmp-dir parabricks/pbrun_fq2bam/{wildcards.sample}_{wildcards.type} &> {log}"

SnakeMake From line 85 of rules/pbrun.smk

shell:
    "{params.cuda} pbrun mutectcaller "
    "--ref {input.fasta} "
    "--in-tumor-bam {input.bam_t} "
    "--tumor-name {wildcards.sample}_T "
    "--in-tumor-recal-file {input.recal_t} "
    "--num-gpus {params.num_gpus} "
    "--out-vcf {output.vcf} "
    "{params.extra} "
    "--tmp-dir parabricks/pbrun_mutectcaller_t/{wildcards.sample} &> {log}"

SnakeMake From line 131 of rules/pbrun.smk

shell:
    "{params.cuda} pbrun mutectcaller "
    "--ref {input.fasta} "
    "--in-tumor-bam {input.bam_t} "
    "--tumor-name {wildcards.sample}_T "
    "--in-tumor-recal-file {input.recal_t} "
    "--in-normal-bam {input.bam_n} "
    "--normal-name {wildcards.sample}_N "
    "--in-normal-recal-file {input.recal_n} "
    "--num-gpus {params.num_gpus} "
    "--out-vcf {output.vcf} "
    "{params.extra} "
    "--tmp-dir parabricks/pbrun_mutectcaller_tn/{wildcards.sample} &> {log}"

SnakeMake From line 179 of rules/pbrun.smk

shell:
    "{params.cuda} pbrun rna_fq2bam "
    "{params.extra} "
    "--genome-lib-dir {input.genome_dir} "
    "--in-fq {params.in_fq} "
    "--num-gpus {params.num_gpus} "
    "--output-dir parabricks/pbrun_rna_fq2bam/ "
    "--out-bam {output.bam} "
    "--out-prefix {wildcards.sample}_{wildcards.type} "
    "--tmp-dir parabricks/pbrun_rna_fq2bam/{wildcards.sample}_{wildcards.type} "
    "{params.extra} "
    "--logfile {log}"