Sam
DataTypes
SamOrBam
DataTypes
SamToFastq
picard
SamtoolsFaidx
samtools
SamtoolsPileup
samtools
SamtoolsTask
samtools
Scatter
ScatterGather
ScatterGather
tasks
ScriptName
BwaK8AltProcessor
SetNmAndUqTags
picard
SortSam
picard
SortVcf
picard
SplitIntervalsForCallingRegions
gatk
SplitNCigarReads
gatk
Strelka
vc
StrelkaDir
Strelka
SummaryMetricsExtension
CollectGcBiasMetrics
sample
FilterSomaticVcf
sampleNames
GetSampleNamesFromVcf
samtools
tasks
secondIn
IntervalListTools
seedLength
BwaAln
BwaBacktrack
slop
TrimPrimers
softClip
ClipOverlappingReads
somatic
FilterFreeBayesCalls
FreeBayes
FreeBayesParallel
somaticPValue
Varscan2Somatic
sort
IntervalListTools
sortOrder
TrimPrimers
FixMateInformation
SortSam
strandFilter
Varscan2Somatic
strategy
GroupReadsByUmi