From 137ecdb3976a68cf0db6dc9212c4e256cf944f63 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 4 Nov 2014 11:42:30 +0100
Subject: [PATCH] Added genotypemergeoption option, needed since Gatk 3.3
Allele mode now also on discovery alleles
---
.../biopet/pipelines/gatk/GatkVariantcalling.scala | 14 +++++++++++---
1 file changed, 11 insertions(+), 3 deletions(-)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
index 465a946ee..e4899798f 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
@@ -84,6 +84,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
if (variantcalling) {
var mergBuffer: SortedMap[String, File] = SortedMap()
+ def mergeList = mergBuffer map { case (key, file) => TaggedFile(removeNoneVariants(file), "name=" + key) }
if (sampleID != null && (useHaplotypecaller.get || config("joint_genotyping", default = false).getBoolean)) {
val hcGvcf = new HaplotypeCaller(this)
@@ -141,10 +142,17 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
mergBuffer += ("9.raw" -> scriptOutput.rawFilterVcfFile)
if (useAllelesOption.get) {
+ val tempFile = if (mergeList.toList.size > 1) {
+ val allelesTemp = CombineVariants(this, mergeList.toList, outputDir + outputName + ".alleles_temp.vcf.gz")
+ allelesTemp.genotypemergeoption = org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.GenotypeMergeType.UNSORTED
+ add(allelesTemp, isIntermediate = true)
+ allelesTemp.out
+ } else mergeList.toList.head
+
val alleleOnly = new CommandLineFunction {
- @Input val input: File = scriptOutput.rawFilterVcfFile
+ @Input val input: File = tempFile
@Output val output: File = outputDir + "raw.allele_only.vcf.gz"
- @Output val outputindex: File = outputDir + "raw.allele_only.vcf.gz.tbi"
+ @Output val outputindex: File = outputDir + "raw.allele__temp_only.vcf.gz.tbi"
def commandLine = "zcat " + input + " | cut -f1,2,3,4,5,6,7,8 | bgzip -c > " + output + " && tabix -pvcf " + output
}
add(alleleOnly, isIntermediate = true)
@@ -181,8 +189,8 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
sv.out
}
- def mergeList = mergBuffer map { case (key, file) => TaggedFile(removeNoneVariants(file), "name=" + key) }
val cvFinal = CombineVariants(this, mergeList.toList, outputDir + outputName + ".final.vcf.gz")
+ cvFinal.genotypemergeoption = org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.GenotypeMergeType.UNSORTED
add(cvFinal)
scriptOutput.finalVcfFile = cvFinal.out
}
--
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