MarkDuplicates
picard
MarkIlluminaAdapters
picard
Megabytes
tasks
MergeBamAlignment
picard
MergeSamFiles
picard
MergeVcfs
picard
MetricsExtension
CollectHsMetrics CollectWgsMetrics EstimateLibraryComplexity MarkDuplicates MarkIlluminaAdapters ValidateSamFile
MoveFile
misc
Mutect1
gatk
Mutect2
gatk
mappedBam
BwaBacktrack
maxAltAlleleInNormalBqSum
Mutect1 Mutect2
maxAltAlleleInNormalCount
Mutect1 Mutect2
maxAltAlleleInNormalFraction
Mutect1 Mutect2
maxAlternateAlleles
HaplotypeCaller
maxCores
BwaAln
maxCoverage
FreeBayes
maxDepth
VerifyBamId
maxFisherStrandValue
FilterVcf
maxThreads
FreeBayes Strelka
memory
FreeBayes
metricsExtension
CollectAlignmentSummaryMetrics CollectGcBiasMetrics CollectHsMetrics CollectInsertSizeMetrics CollectMultipleMetrics CollectTargetedPcrMetrics CollectWgsMetrics EstimateLibraryComplexity MarkDuplicates MarkIlluminaAdapters PicardMetricsTask ValidateSamFile
metricsFile
PicardMetricsTask
minAlternateAlleleFraction
FreeBayesSomatic
minDP
GenotypeConcordance
minDepth
FilterVcf
minGQ
GenotypeConcordance
minGenotypeQuality
FilterVcf
minHetAlleleBalance
FilterVcf
minIdenticalBases
EstimateLibraryComplexity
minIdenticalBasesFor
EstimateLibraryComplexity
minMapq
VerifyBamId
minQ
VerifyBamId
minQd
FilterVcf
minQual
FilterFreeBayesCalls
minRepeatEntropy
FreeBayes
minThreads
FreeBayes Strelka
minimumPercent
CollectInsertSizeMetrics
minimumVariantFrequency
Varscan2Somatic
misc
tasks
missingSitesAreHomRef
GenotypeConcordance