From 03232d6aee841c48dbb0b4b2abaad37160d4cfc2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ant=C3=B3nio=20Paulo?= <antonio.do.paulo@ist.utl.pt>
Date: Mon, 5 Aug 2019 17:49:22 +0200
Subject: [PATCH] add GATK3 CombineVariants as a task
---
gatk.wdl | 48 ++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 48 insertions(+)
diff --git a/gatk.wdl b/gatk.wdl
index 12d8dba..b4a210d 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -505,3 +505,51 @@ task SplitNCigarReads {
memory: ceil(memory * memoryMultiplier)
}
}
+
+task CombineVariants {
+ input {
+ String installDir = "/usr"
+
+ File referenceFasta
+ File referenceFastaFai
+ File referenceFastaDict
+ String genotypeMergeOption = "UNIQUIFY"
+ String filteredRecordsMergeType = "KEEP_IF_ANY_UNFILTERED"
+ Array[String]+ identifiers
+ Array[File]+ variantVcfs # follow "identifiers" array order
+ Array[File]+ variantIndexes
+ String outputPath
+
+ Int memory = 4
+ Float memoryMultiplier = 1.5
+ String dockerImage = "broadinstitute/gatk3:3.8-1"
+ }
+
+ command <<<
+ set -e -o pipefail
+ mkdir -p $(dirname "~{outputPath}")
+
+ # build "-V:<ID> <file.vcf>" arguments according to IDs and VCFs to merge
+ ids=(~{sep=" " identifiers})
+ vars=(~{sep=" " variantVcfs})
+ V_lines=`for ((i=0;i<${#ids[@]};++i)); do printf -- "-V:%s %s " "${ids[i]}" "${vars[i]}"; done`
+
+ java -Xmx~{memory}G -jar ~{installDir}/GenomeAnalysisTK.jar \
+ -T CombineVariants \
+ -R ~{referenceFasta} \
+ --genotypemergeoption ~{genotypeMergeOption} \
+ --filteredrecordsmergetype ~{filteredRecordsMergeType} \
+ --out ~{outputPath} \
+ $V_lines
+ >>>
+
+ output {
+ File combinedVcf = outputPath
+ File combinedVcfIndex = outputPath + ".tbi"
+ }
+
+ runtime {
+ docker: dockerImage
+ memory: ceil(memory * memoryMultiplier)
+ }
+}
\ No newline at end of file
--
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