From 6a0df09174529789a4bb6651ae992d0758d6a7eb Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Thu, 26 Jul 2018 16:25:57 +0200
Subject: [PATCH] add vcfStats and Mutect2
---
biopet.wdl | 68 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
gatk.wdl | 45 ++++++++++++++++++++++++++++++++++++
2 files changed, 113 insertions(+)
diff --git a/biopet.wdl b/biopet.wdl
index 36d6f2a..a3ecdd0 100644
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -417,3 +417,71 @@ task ValidateVcf {
memory: ceil(memory * memoryMultiplier)
}
}
+
+task VcfStats {
+ input {
+ File vcfFile
+ File vcfIndex
+ File refFasta
+ File refFastaIndex
+ File refDict
+ String outDir
+ File? intervals
+ Array[String]+? infoTags
+ Array[String]+? genotypeTags
+ Int? sampleToSampleMinDepth
+ Int? binSize
+ Int? maxContigsInSingleJob
+ Boolean writeBinStats = false
+ Int localThreads = 1
+ Boolean notWriteContigStats = false
+ Boolean skipGeneral = false
+ Boolean skipGenotype = false
+ Boolean skipSampleDistributions = false
+ Boolean skipSampleCompare = false
+ String? sparkMaster
+ Int? sparkExecutorMemory
+ Array[String]+? sparkConfigValues
+
+ Int memory = 4
+ Float memoryMultiplier = 2.0
+ File? toolJar
+ String? preCommand
+ }
+
+ String toolCommand = if defined(toolJar)
+ then "java -Xmx" + memory + "G -jar " + toolJar
+ else "biopet-vcfstats -Xmx" + memory + "G"
+
+ command {
+ set -e -o pipefail
+ ~{preCommand}
+ ~{toolCommand} \
+ -I ~{vcfFile} \
+ -R ~{refFasta} \
+ -o ~{outDir} \
+ -t ~{localThreads} \
+ ~{"--intervals " + intervals} \
+ ~{true="--infoTag" false="" defined(infoTags)} ~{sep=" --infoTag " infoTags} \
+ ~{true="--genotypeTag" false="" defined(genotypeTags)} ~{sep=" --genotypeTag "
+ genotypeTags} \
+ ~{"--sampleToSampleMinDepth " + sampleToSampleMinDepth} \
+ ~{"--binSize " + binSize} \
+ ~{"--maxContigsInSingleJob " + maxContigsInSingleJob} \
+ ~{true="--writeBinStats" false="" writeBinStats} \
+ ~{true="--notWriteContigStats" false="" notWriteContigStats} \
+ ~{true="--skipGeneral" false="" skipGeneral} \
+ ~{true="--skipGenotype" false="" skipGenotype} \
+ ~{true="--skipSampleDistributions" false="" skipSampleDistributions} \
+ ~{true="--skipSampleCompare" false="" skipSampleCompare} \
+ ~{"--sparkMaster " + sparkMaster} \
+ ~{"--sparkExecutorMemory " + sparkExecutorMemory} \
+ ~{true="--sparkConfigValue" false="" defined(sparkConfigValues)} ~{
+ sep=" --sparkConfigValue" sparkConfigValues}
+ }
+
+ runtime {
+ cpu: localThreads
+ memory: ceil(memory * memoryMultiplier)
+ }
+}
diff --git a/gatk.wdl b/gatk.wdl
index 68281f3..75e45e5 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -293,6 +293,51 @@ task HaplotypeCallerGvcf {
}
}
+task MuTect2 {
+ input {
+ String? preCommand
+
+ Array[File]+ inputBams
+ File inputBamIndex
+ File refFasta
+ File refFastaIndex
+ File refDict
+ String outputVcf
+ String tumorSample
+ String? normalSample
+ Array[File]+ intervals
+
+ String? gatkJar
+ Int memory = 4
+ Float memoryMultiplier = 3
+ }
+
+ String toolCommand = if defined(gatkJar)
+ then "java -Xmx" + memory + "G -jar " + gatkJar
+ else "gatk --java-options -Xmx" + memory + "G"
+
+ command {
+ set -e -o pipefail
+ ~{preCommand}
+ ~{toolCommand} \
+ Mutect2 \
+ -R ~{refFasta} \
+ -I ~{sep=" -I " inputBams} \
+ -tumor ~{tumorSample} \
+ ~{"-normal " + normalSample} \
+ -O ~{outputVcf} \
+ -L ~{sep=" -L " intervals}
+ }
+
+ output {
+ File vcfFile = outputVcf
+ }
+
+ runtime {
+ memory: ceil(memory * memoryMultiplier)
+ }
+}
+
task SplitNCigarReads {
input {
String? preCommand
--
GitLab