Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

add ignore_soft_clipped_bases option #230

Merged
merged 3 commits into from
Jul 14, 2020
Merged

add ignore_soft_clipped_bases option #230

Show file tree
Hide file tree
Changes from 2 commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
e51be25
added dont_use_soft_clipped_bases option
pcantalupo Jul 13, 2020
bacf835
added default value
pcantalupo Jul 13, 2020
aa0162d
Apply suggestions from code review
pcantalupo Jul 13, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 3 additions & 0 deletions main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -94,6 +94,7 @@ def helpMessage() {
Default: ${params.cf_ploidy}
--cf_window [int] Control-FREEC window size
Default: Disabled
--dont_use_soft_clipped_bases [bool] Do not analyze soft clipped bases in the reads for GATK Mutect2
pcantalupo marked this conversation as resolved.
Show resolved Hide resolved
--no_gvcf [bool] No g.vcf output from GATK HaplotypeCaller
--no_strelka_bp [bool] Will not use Manta candidateSmallIndels for Strelka (not recommended by Best Practices)
--pon [file] Panel-of-normals VCF (bgzipped) for GATK Mutect2 / Sentieon TNscope
Expand Down Expand Up @@ -2465,6 +2466,7 @@ process Mutect2 {
// https://gatkforums.broadinstitute.org/gatk/discussion/11136/how-to-call-somatic-mutations-using-gatk4-mutect2
PON = params.pon ? "--panel-of-normals ${pon}" : ""
intervalsOptions = params.no_intervals ? "" : "-L ${intervalBed}"
softclippedOption = params.dont_use_soft_clipped_bases ? "--dont-use-soft-clipped-bases true" : ""
maxulysse marked this conversation as resolved.
Show resolved Hide resolved
pcantalupo marked this conversation as resolved.
Show resolved Hide resolved
"""
# Get raw calls
gatk --java-options "-Xmx${task.memory.toGiga()}g" \
Expand All @@ -2473,6 +2475,7 @@ process Mutect2 {
-I ${bamTumor} -tumor ${idSampleTumor} \
-I ${bamNormal} -normal ${idSampleNormal} \
${intervalsOptions} \
${softclippedOption} \
maxulysse marked this conversation as resolved.
Show resolved Hide resolved
pcantalupo marked this conversation as resolved.
Show resolved Hide resolved
--germline-resource ${germlineResource} \
${PON} \
-O ${intervalBed.baseName}_${idSampleTumor}_vs_${idSampleNormal}.vcf
Expand Down
1 change: 1 addition & 0 deletions nextflow.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -66,6 +66,7 @@ params {
no_strelka_bp = null // Strelka will use Manta candidateSmallIndels if available
pon = false // No default PON (Panel of Normals) file for GATK Mutect2 / Sentieon TNscope
pon_index = false // No default PON index for GATK Mutect2 / Sentieon TNscope
dont_use_soft_clipped_bases = null // GATK Mutect2
pcantalupo marked this conversation as resolved.
Show resolved Hide resolved

// Annotation
annotate_tools = null // Only with --step annotate
Expand Down