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Add possibility to run HaplotypeCaller without dbsnp #182

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Apr 15, 2020
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Add possibility to run HaplotypeCaller without dbsnp #182

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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,7 @@ Piellorieppe is one of the main massif in the Sarek National Park.
- [#176](https://github.com/nf-core/sarek/pull/176) - Add empty `custom` genome in `genomes.config` to allow genomes that are not in `AWS iGenomes`
- [#179](https://github.com/nf-core/sarek/pull/179) - Add `FreeBayes` germline variant calling
- [#180](https://github.com/nf-core/sarek/pull/180) - Now saving Mapped Bams (and creating TSV) in minimal setting
- [#182](https://github.com/nf-core/sarek/pull/182) - Add possibility to run `HaplotypeCaller` without `dbsnp` so it can be used to actually generate vcfs to build a set of known sites (cf [gatkforums](https://gatkforums.broadinstitute.org/gatk/discussion/1247/what-should-i-use-as-known-variants-sites-for-running-tool-x))

### Changed - [2.6dev]

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8 changes: 5 additions & 3 deletions main.nf
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Expand Up @@ -1223,7 +1223,7 @@ process IndexBamFile {

tag {idPatient + "-" + idSample}

publishDir "${params.outdir}/Preprocessing/${idSample}/Mapped/${it}", mode: params.publish_dir_mode
publishDir "${params.outdir}/Preprocessing/${idSample}/Mapped", mode: params.publish_dir_mode

input:
set idPatient, idSample, file(bam) from bam_mapped_merged_to_index
Expand Down Expand Up @@ -1819,13 +1819,14 @@ process HaplotypeCaller {

script:
intervalsOptions = params.no_intervals ? "" : "-L ${intervalBed}"
dbsnpOptions = params.dbsnp ? "--D ${dbsnp}" : ""
"""
gatk --java-options "-Xmx${task.memory.toGiga()}g -Xms6000m -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10" \
HaplotypeCaller \
-R ${fasta} \
-I ${bam} \
${intervalsOptions} \
-D ${dbsnp} \
${dbsnpOptions} \
-O ${intervalBed.baseName}_${idSample}.g.vcf \
-ERC GVCF
"""
Expand Down Expand Up @@ -1857,6 +1858,7 @@ process GenotypeGVCFs {
script:
// Using -L is important for speed and we have to index the interval files also
intervalsOptions = params.no_intervals ? "" : "-L ${intervalBed}"
dbsnpOptions = params.dbsnp ? "--D ${dbsnp}" : ""
"""
gatk --java-options -Xmx${task.memory.toGiga()}g \
IndexFeatureFile \
Expand All @@ -1866,7 +1868,7 @@ process GenotypeGVCFs {
GenotypeGVCFs \
-R ${fasta} \
${intervalsOptions} \
-D ${dbsnp} \
${dbsnpOptions} \
-V ${gvcf} \
-O ${intervalBed.baseName}_${idSample}.vcf
"""
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