RealignerTargetCreator
gatk
RemoveSamTags
fgbio
RevertSam
picard
RootDir
VarDictJava
RootDirConfigKey
VarDictJava
r1Fastq
BwaSampe
BwaSamse
r1Sai
BwaSampe
BwaSamse
r2Fastq
BwaSampe
r2Sai
BwaSampe
rawTag
GroupReadsByUmi
readGroupId
CallDuplexConsensusReads
CallMolecularConsensusReads
readNamePrefix
CallDuplexConsensusReads
CallMolecularConsensusReads
readStructures
ExtractUmisFromBam
ref
BwaAln
BwaBacktrack
BwaIndex
BwaSampe
BwaSamse
ClipOverlappingReads
ErrorRateByReadPosition
FilterConsensusReads
TrimPrimers
GatkTask
CollectSequencingArtifactMetrics
SamtoolsFaidx
FilterFreeBayesCalls
FreeBayes
FreeBayesParallel
Strelka
regionSize
FreeBayes
rejects
CallMolecularConsensusReads
rnaMode
HaplotypeCaller
run
SplitIntervalsForCallingRegions
CalculateDownsamplingProportion
DeleteFiles
DeleteVcfs
GetNumPfReads
GetSampleNamesFromVcf
DeleteBam