accuracy
DownsampleSam
action
IntervalListTools
addJeanLucArgs
FilterBam
GenerateRegionsFromFasta
JeanLucTask
addPicardArgs
JeanLucTask
CollectAlignmentSummaryMetrics
CollectGcBiasMetrics
CollectHsMetrics
CollectInsertSizeMetrics
CollectMultipleMetrics
CollectTargetedPcrMetrics
CollectVariantCallingMetrics
CollectWgsMetrics
DownsampleSam
EstimateLibraryComplexity
FastqToSam
FifoBuffer
FilterVcf
GenotypeConcordance
IntervalListToBed
IntervalListTools
MarkDuplicates
MarkIlluminaAdapters
MergeBamAlignment
MergeSamFiles
MergeVcfs
PicardTask
SamToFastq
SortSam
ValidateSamFile
addSubcommandArgs
SamtoolsPileup
SamtoolsTask
addWalkerArgs
GatkTask
GenotypeSingleGvcf
HaplotypeCaller
IndelRealigner
Mutect1
Mutect2
RealignerTargetCreator
SplitNCigarReads
apply
FastqToUnmappedSam
SamToFastq
args
BwaAln
BwaK8AltProcessor
BwaMem
BwaSampe
GatkTask
VerifyBamId
PicardTask
SamtoolsTask
FilterFreeBayesCalls
Varscan2Somatic