MakeDirectory
misc
MarkDuplicates
picard
MarkIlluminaAdapters
picard
Megabytes
tasks
MergeBamAlignment
picard
MergeSamFiles
picard
MergeVcfs
picard
MetricsExtension
CollectBaseDistributionByCycle
CollectHsMetrics
CollectWgsMetrics
EstimateLibraryComplexity
MarkDuplicates
MarkIlluminaAdapters
ValidateSamFile
MoveFile
misc
Mutect1
gatk
Mutect2
gatk
map
Scatter
mappedBam
BwaBacktrack
maxAltAlleleInNormalBqSum
Mutect1
Mutect2
maxAltAlleleInNormalCount
Mutect1
Mutect2
maxAltAlleleInNormalFraction
Mutect1
Mutect2
maxAlternateAlleles
HaplotypeCaller
maxBaseErrorRate
FilterConsensusReads
maxCores
BwaAln
maxCoverage
FreeBayes
FreeBayesParallel
maxDepth
VerifyBamId
maxDiffOrMissingProb
BwaAln
BwaBacktrack
maxFisherStrandValue
FilterVcf
maxNoCallFraction
FilterConsensusReads
maxReadErrorRate
FilterConsensusReads
maxReadsInRegionPerSample
HaplotypeCaller
maxThreads
FreeBayes
FreeBayesParallel
Strelka
memory
FreeBayes
FreeBayesParallel
memoryPerThread
IlluminaBasecallsToSam
metricsExtension
CollectAlignmentSummaryMetrics
CollectBaseDistributionByCycle
CollectGcBiasMetrics
CollectHsMetrics
CollectIlluminaBasecallingMetrics
CollectInsertSizeMetrics
CollectMultipleMetrics
CollectQualityYieldMetrics
CollectSequencingArtifactMetrics
CollectTargetedPcrMetrics
CollectWgsMetrics
EstimateLibraryComplexity
ExtractIlluminaBarcodes
MarkDuplicates
MarkIlluminaAdapters
PicardMetricsTask
ValidateSamFile
metricsFile
PicardMetricsTask
minAlternateAlleleFraction
FreeBayesParallel
FreeBayesSomatic
minBaseQuality
ErrorRateByReadPosition
FilterSomaticVcf
Mutect1
minBq
CollectSequencingArtifactMetrics
minDP
GenotypeConcordance
minDepth
FilterVcf
minGQ
GenotypeConcordance
minGenotypeQuality
FilterVcf
minHetAlleleBalance
FilterVcf
minIdenticalBases
EstimateLibraryComplexity
minIdenticalBasesFor
EstimateLibraryComplexity
minInputBaseQuality
CallDuplexConsensusReads
CallMolecularConsensusReads
minMapQ
FilterSomaticVcf
GroupReadsByUmi
minMappingQuality
ErrorRateByReadPosition
minMapq
VerifyBamId
minMq
CollectSequencingArtifactMetrics
minPruning
HaplotypeCaller
minQ
VerifyBamId
minQd
FilterVcf
minQual
FilterFreeBayesCalls
minQuality
FilterConsensusReads
minReads
CallMolecularConsensusReads
FilterConsensusReads
minReadsPerAlignmentStart
HaplotypeCaller
minRepeatEntropy
FreeBayes
FreeBayesParallel
minThreads
FreeBayes
FreeBayesParallel
Strelka
minimumAf
Mutect1
minimumPercent
CollectInsertSizeMetrics
minimumVariantFrequency
Varscan2Somatic
misc
tasks
missingSitesAreHomRef
GenotypeConcordance