// Mutect2 joint somatic variant calling workflow
digraph Mutect2JointSomaticWorkflow {
	node [shape=record]
	createCallRegions [label="createCallRegions (Create genomic call regions)"]
	mutect2 [label="mutect2 (GatkMutect2)"]
	concat [label="concat (BCFTools: Concat)"]
	indexUnfiltered [label="indexUnfiltered (BCFTools: Index)"]
	learn [label="learn (GATK4: LearnReadOrientationModel)"]
	mergeMutect2 [label="mergeMutect2 (GATK4: MergeMutectStats)"]
	pileup [label="pileup (GATK4: GetPileupSummaries)"]
	contamination [label="contamination (GATK4: CalculateContamination)"]
	filtering [label="filtering (GATK4: GetFilterMutectCalls)"]
	normalise [label="normalise (BCFTools: Normalize)"]
	indexFiltered [label="indexFiltered (BCFTools: Index)"]
	createCallRegions -> mutect2
	mutect2 -> concat
	concat -> indexUnfiltered
	mutect2 -> learn
	mutect2 -> mergeMutect2
	pileup -> contamination
	mergeMutect2 -> filtering
	learn -> filtering
	contamination -> filtering
	indexUnfiltered -> filtering
	filtering -> normalise
	normalise -> indexFiltered
}
