Joint germline structural variant and copy number variant calling using Delly
java -jar cromwell.jar run dellyGermline.wdl --inputs inputs.json
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 |
Parameter | Value | Default | Description |
---|
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 |
Output | Type | Description |
---|---|---|
germlineSVs |
File | Filtered vcf file containing PASS structural variant calls |
germlineCNVs |
File | Filtered vcf file containing copy number variant calls |
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
For support, please file an issue on the Github project or send an email to gsi@oicr.on.ca .
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