SV calling pipeline

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HiFi-sv-snakemake

A snakemake pipeline for structural variant(SV) analysis base on HiFi reads
With it, you can get a set of SV dataset including five types, which are Insertion , Deletion , Inversion , Duplication , and Translocation .

Input files
Dependencies
Examples
Overview of the workflow

Input files

To use the pipeline you should first copy the Snakefile and config.yaml files in the working directory. Then prepare the following files:

a reference file named {genome}.fa
a assembled genome file named {sample}.fa
a HiFi reads fastq file named {sample}.fq.gz

The {genome} and {sample} labels should match the label in the configuration (config.yaml file or in the command line).

Dependencies

Conda environment files containing the dependencies can be found in the envs directory. These can be automatically installed and managed by providing the --use-conda argument to snakemake: snakemake --use-conda ... .
The folder scripts contains python scripts and text necessary for the pipeline.

Examples

This pipeline mainly contains four steps:

read_map_all to obtain all necessary ailgnment file for SV calling.

snakemake --configfile config.yaml --cores 32 --use-conda read_map_all

call_original_all to calling SV by mutiple callers and aligners.

snakemake --configfile config.yaml --cores 16 --use-conda call_original_all

call_filter_all to filter all SV detasets.

snakemake --configfile config.yaml --cores 5 --use-conda call_filter_all

final_results_all to get variant suitable for each SV type.

snakemake --configfile config.yaml --cores 16 --use-conda final_results_all

In this pipeline, we defined:
Insertion: detected by NGMLR + pbmm2 - SVIM ;
Deletion: detected by NGMLR + pbmm2 - Sniffles and Assemblytics ;
Inversion: detected by NGMLR - cuteSV + Sniffles ;
Duplication: detected by pbmm2 - pbsv + cuteSV ;
Tranlocation: detedcted by NGMLR + pbmm2 - pbsv + Sniffles + cuteSV and SyRI .

Overview of the workflow

We can easily visualize the workflow with Snakemake .

Rule graph

snakemake --rulegraph --configfile config.yaml -f final_results_all | dot -Tsvg > rulegraph.svg

DAG of jobs

snakemake -np -f final_results_all --configfile config.yaml --dag | dot -Tsvg > DAGgraph.svg

Code Snippets

shell:
    'ngmlr -r {input.ref} -q {input.fq} -t {threads} -x pacbio --rg-sm {wildcards.sample} --rg-lb {params.para} --rg-pl PacBio -o {output} 2> {log}'

SnakeMake NGMLR From line 71 of main/Snakefile

shell:
    "pbmm2 align {input} {output} --unmapped --preset CCS -N 2 --sort --rg '@RG\\tID:{wildcards.sample}\\tSM:{wildcards.sample}\\tLB:{params.para}\\tPL:PB' 2> {log}"

SnakeMake pbmm2 From line 86 of main/Snakefile

shell:
    'samtools sort {input.bam_ngmlr} -o {output.sort_ngmlr} | samtools index 2> {log}' \
    'samtools sort {input.bam_pbmm2} -o {output.sort_pbmm2} | samtools index 2>> {log}'

SnakeMake SAMtools From line 104 of main/Snakefile

shell:
    'nucmer --maxmatch {params.para} {input.ref} {input.asm} -p {wildcards.sample}-{params.name} -t {threads} 2> {log}' \
    'mv {wildcards.sample}-{params.name}.delta {output}'

SnakeMake mummer2circos From line 125 of main/Snakefile

shell:
    'minimap2 -ax asm5 --eqx {input.ref} {input.asm} > {output.sam} | samtools view -b -o {output.bam} >2 {log}'

SnakeMake SAMtools Minimap2 From line 141 of main/Snakefile

shell:
    'trf {input.ref} {params.para} 2> {log.tdm}' \
    'pbsv discover {input.bam} --tandem-repeats {output.repeat} {output.svsig} 2> {log.sv}' \
    'pbsv call --ccs -x {params.depth} {input.ref} {output.svsig} {output.vcf} 2>> {log.sv}'

SnakeMake pbsv TRF From line 164 of main/Snakefile

shell:
    'svim alignment --sequence_alleles --read_names {input.ref} {input.bam} {params.outdir}/ 2> {log}' \
    'mv {params.outdir}/final_results.vcf {output}'

SnakeMake svim From line 182 of main/Snakefile

shell:
    'samtools calmd -u {input.pbmm2_bam} {input.ref} > {output.pbmm2_MD}' \
    'sniffles --skip_parameter_estimation -s {params.para} --ccs_reads -m {input.ngmlr_bam} -v {output.vcf_ngmlr} 2> {log.log_ngmlr}' \
    'sniffles --skip_parameter_estimation -s {params.para} --ccs_reads -m {output.pbmm2_MD} -v {output.vcf_pbmm2} 2> {log.log_pbmm2}'

SnakeMake SAMtools sniffles From line 204 of main/Snakefile

shell:
    'samtools calmd -u {input.pbmm2_bam} {input.ref} > {output.pbmm2_MD}' \
    'sniffles --skip_parameter_estimation -s {params.para} --ccs_reads -m {input.ngmlr_bam} -v {output.vcf_ngmlr} 2> {log.log_ngmlr}' \
    'sniffles --skip_parameter_estimation -s {params.para} --ccs_reads -m {output.pbmm2_MD} -v {output.vcf_pbmm2} 2> {log.log_pbmm2}'

SnakeMake SAMtools sniffles From line 225 of main/Snakefile

shell:
    'mkdir {params.work_dir}' \
    'cuteSV {input} {output} {params.work_dir} --max_cluster_bias_INS 1000 --diff_ratio_merging_INS 0.9 --max_cluster_bias_DEL 1000 --diff_ratio_merging_DEL 0.5 --threads {threads} --sample {wildcards.sample}-{params.map_name} --min_support 10 --genotype 2> {log}'

SnakeMake cuteSV From line 243 of main/Snakefile

shell:
    'gzip {input} | scripts/Assemblytics {wildcards.sample}-{params.name} 10000 20 100000 2> {log}' \
    'mv {wildcards.sample}-{params.name}/{wildcards.sample}-{params.name}.Assemblytics_structural_variants.bed {output}'

SnakeMake From line 260 of main/Snakefile

shell:
    'python ref_chr.py -i {input.ref} -o {output.ref_chr} -c {params.max_chr}' \
    'python asm_chr.py -i {input.asm} -o {output.asm_chr}' \
    'syri -c {input.bam} -r {output.ref_chr} -q {output.asm_chr} -k -F B --nosnp 2> {log}' \
    'mv syri.vcf {output.vcf}'

SnakeMake From line 279 of main/Snakefile

shell:
    'python svim_ins_filter.py -i {input} -q {params.qual} -o {output}'

SnakeMake From line 300 of main/Snakefile

shell:
    'ls {input} > sample_files_ins' \
    'SURVIVOR merge sample_files_ins 1000 1 1 1 0 20 {output} 2> {log}'

SnakeMake SURVIVOR From line 313 of main/Snakefile

shell:
    'python assemblytics_format_change.py -i {input.bed} -a {input.txt} -o {output.vcf_temp}' \
    'bcftools norm -f {input.ref} -m-both -c s -o {output.norm} {output.vcf_temp}' \
    'python genotype.py -i {output.vcf_temp} -o {output.vcf}'

SnakeMake BCFtools From line 329 of main/Snakefile

run:
    shell('python sniffles_del_fileter.py -i {input} -o {output}')

SnakeMake From line 339 of main/Snakefile

run:
    shell('(ls {input} > sample_files_del)')
    shell('(SURVIVOR merge sample_files_del 1000 1 1 1 0 20 {output}) 2> {log}')

SnakeMake From line 351 of main/Snakefile

run:
    shell('python sniffles_inv_fileter.py -i {input.Sniffles} -o {output.Sniffles_vcf}')
    shell('python cutesv_inv_fliter.py -i {input.cuteSV} -o {output.cuteSV_vcf}')

SnakeMake From line 366 of main/Snakefile

run:
    shell('(ls {input} > sample_files_inv)')
    shell('(SURVIVOR merge sample_files_inv 1000 1 1 1 0 20 {output}) 2> {log}')

SnakeMake From line 378 of main/Snakefile

run:
    shell('python pbsv_dup_fileter.py -i {input.pbsv} -o {output.pbsv_vcf}')
    shell('python cutesv_dup_fliter.py -i {input.cuteSV} -o {output.cuteSV_vcf}')

SnakeMake From line 392 of main/Snakefile

run:
    shell('(ls {input} > sample_files_dup)')
    shell('(SURVIVOR merge sample_files_dup 1000 1 1 1 0 20 {output}) 2> {log}')

SnakeMake From line 404 of main/Snakefile

run:
    shell('python syri_tra_filter.py -i {input} -o {output}')

SnakeMake From line 416 of main/Snakefile

run:
    shell('python pbsv_tra_filter.py -i {input.pbsv} -o {output.pbsv_vcf}')
    shell('python sniffles_tra_filter.py -i {input.Sniffles} -o {output.Sniffles_vcf}')
    shell('python cutesv_tra_filter.py -i {input.cuteSV} -o {output.cuteSV_vcf}')

SnakeMake From line 428 of main/Snakefile

run:
    shell('(ls {input} > sample_files_tra)')
    shell('(SURVIVOR merge sample_files_tra 1000 2 1 1 0 20 {output}) 2> {log}')

SnakeMake From line 446 of main/Snakefile

run:
    shell('python tra_remove_repeat.py -i {input} -o {output}')

SnakeMake From line 455 of main/Snakefile

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Created: 1yr ago

Updated: 1yr ago

Maitainers: public

URL: https://github.com/Triciasnow/HiFi-sv-snakemake

Name: hifi-sv-snakemake

Version: 1

Badge:

Insert copied code into your website to add a link to this workflow.

License: Apache License 2.0

Keywords:

mummer2circos pbsv sniffles svim BCFtools Minimap2 NGMLR pbmm2 SAMtools Snakemake TRF cuteSV SURVIVOR

Future updates

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