diff --git a/gatk.wdl b/gatk.wdl index 51cc133869202dc7e5e28880e44c618b56eff984..12d8dbad72388e488c640603cc0dd0493bc5c691 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