/dellyGermline

Call germline SVs using Delly

Primary LanguageWDL

dellyGermline

Joint germline structural variant and copy number variant calling using Delly

Overview

Dependencies

Usage

Cromwell

java -jar cromwell.jar run dellyGermline.wdl --inputs inputs.json

Inputs

Required workflow parameters:

Parameter Value Description
reference String The genome reference build. for example: hg19, hg38
inputSamples Array[inputSamples] Collection of BAM, BAI, and VCF files for >= 20 samples

Optional workflow parameters:

Parameter Value Default Description

Optional task parameters:

Parameter Value Default Description
mergeSVSites.jobMemory Int 12 Memory allocated for this job
mergeSVSites.timeout Int 12 Timeout in hours, needed to override imposed limits
svGenotype.jobMemory Int 12 Memory allocated for this job
svGenotype.timeout Int 12 Timeout in hours, needed to override imposed limits
mergeSVSamples.jobMemory Int 12 Memory allocated for this job
mergeSVSamples.timeout Int 12 Timeout in hours, needed to override imposed limits
svFilter.jobMemory Int 12 Memory allocated for this job
svFilter.timeout Int 12 Timeout in hours, needed to override imposed limits
callCNV.jobMemory Int 12 Memory allocated for this job
callCNV.timeout Int 12 Timeout in hours, needed to override imposed limits
mergeCNVSites.jobMemory Int 12 Memory allocated for this job
mergeCNVSites.timeout Int 12 Timeout in hours, needed to override imposed limits
cnvGenotype.jobMemory Int 12 Memory allocated for this job
cnvGenotype.timeout Int 12 Timeout in hours, needed to override imposed limits
mergeCNVSamples.jobMemory Int 12 Memory allocated for this job
mergeCNVSamples.timeout Int 12 Timeout in hours, needed to override imposed limits
cnvFilter.jobMemory Int 12 Memory allocated for this job
cnvFilter.timeout Int 12 Timeout in hours, needed to override imposed limits

Outputs

Output Type Description
germlineSVs File Filtered vcf file containing PASS structural variant calls
germlineCNVs File Filtered vcf file containing copy number variant calls

Commands

This section lists command(s) run by the dellyGermline workflow

  • Running dellyGermline

=== Merge SV Sites Across Samples ===.

    set -eu -o pipefail
    delly merge -o MERGED_SV_SITES_BCF INPUT_VCFS

=== Genotype Samples Across Merged SV Sites ===.

    set -eu -o pipefail
    delly call -g REFERENCE_GENOME -v MERGED_SV_SITES_BCF -o GENOTYPED_BCF -x DELLY_EXCLUDE INPUT_BAM

=== Merge Genotyped Samples into Single BCF ===.

    set -eu -o pipefail
    bcftools merge -m id -O b -o MERGED_GENOTYPED_BCF GENOTYPED_BCFS

=== Apply Germline Filter to Merged BCF with SV Calls and Convert to VCF ===.

    set -eu -o pipefail
    bcftools index MERGED_GENOTYPED_BCF
    delly filter -f germline -o GERMLINE_SV_BCF MERGED_GENOTYPED_BCF
    bcftools view -O v -o GERMLINE_SV_VCF GERMLINE_SV_BCF

=== Call CNVs for Samples While Refining Breakpoints Using the SV Calls ===.

    set -eu -o pipefail
    delly cnv -o CNV_BCF -g REFERENCE_GENOME -m MAPPABILITY_MAP -l GERMLINE_SV_BCF INPUT_BAM

=== Merge CNV Sites Across Samples ===.

    set -eu -o pipefail
    delly merge -e -p -o MERGED_SITES_CNV_BCF -m 1000 -n 100000 CNV_BCFS

=== Genotype Samples Across Merged CNV Sites ===.

    set -eu -o pipefail
    delly cnv -u -v MERGED_SITES_CNV_BCF -g REFERENCE_GENOME -m MAPPABILITY_MAP -o GENOTYPED_BCF INPUT_BAM

=== Merge Genotyped CNV Samples into Single BCF ===.

    set -eu -o pipefail
    bcftools merge -m id -O b -o MERGED_GENOTYPED_CNV_BCF GENOTYPED_BCFS

=== Apply Germline Filter to Merged BCF with CNV Calls and Convert to VCF ===.

    set -eu -o pipefail
    bcftools index MERGED_GENOTYPED_CNV_BCF
    delly classify -f germline -o GERMLINE_CNVS_BCF MERGED_GENOTYPED_CNV_BCF
    bcftools view -O v -o GERMLINE_CNVS_VCF GERMLINE_CNVS_BCF

Support

For support, please file an issue on the Github project or send an email to gsi@oicr.on.ca .

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