From 70ae489e1b0f3ffd6f76621fbc8a62e4f498bfc9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ant=C3=B3nio=20Paulo?= <antonio.do.paulo@ist.utl.pt>
Date: Sun, 4 Aug 2019 15:14:26 +0200
Subject: [PATCH] add GATK FilterMutectCalls as a task
---
gatk.wdl | 51 ++++++++++++++++++++++++++++++++++++++++++++++++++-
1 file changed, 50 insertions(+), 1 deletion(-)
diff --git a/gatk.wdl b/gatk.wdl
index 51cc133..12d8dba 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -318,7 +318,7 @@ task LearnReadOrientationModel {
}
output {
- File artifactPriorTable = "artifact-priors.tar.gz"
+ File artifactPriorsTable = "artifact-priors.tar.gz"
}
runtime {
@@ -420,6 +420,55 @@ task CalculateContamination {
}
}
+task FilterMutectCalls {
+ input {
+ File referenceFasta
+ File referenceFastaFai
+ File referenceFastaDict
+ File unfilteredVcf
+ File unfilteredVcfIndex
+ String outputVcf
+ File? contaminationTable
+ File? mafTumorSegments
+ File? artifactPriors
+ Int uniqueAltReadCount = 4
+ File mutect2Stats
+ String? extraArgs
+
+ Int memory = 4
+ Float memoryMultiplier = 1.5
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
+ }
+
+ command {
+ set -e
+ gatk --java-options -Xmx~{memory}G \
+ FilterMutectCalls \
+ -R ~{referenceFasta} \
+ -V ~{unfilteredVcf} \
+ -O ${outputVcf} \
+ ~{"--contamination-table " + contaminationTable} \
+ ~{"--tumor-segmentation " + mafTumorSegments} \
+ ~{"--ob-priors " + artifactPriors} \
+ ~{"--unique-alt-read-count " + uniqueAltReadCount} \
+ ~{"-stats " + mutect2Stats} \
+ --filtering-stats "filtering.stats" \
+ --showHidden \
+ ~{extraArgs}
+ }
+
+ output {
+ File filteredVcf = outputVcf
+ File filteredVcfIndex = outputVcf + ".tbi"
+ File filteringStats = "filtering.stats"
+ }
+
+ runtime {
+ docker: dockerImage
+ memory: ceil(memory * memoryMultiplier)
+ }
+}
+
task SplitNCigarReads {
input {
File inputBam
--
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