annotateTargets	annotateTargets
bootstrapResults	bootstrapResults
calculateBamCoverageByInterval	calculateBamCoverageByInterval
calculateLogRatio	calculateLogRatio
calculateMappingBiasGatk4	calculateMappingBiasGatk4
calculateMappingBiasVcf	calculateMappingBiasVcf
calculatePowerDetectSomatic	calculatePowerDetectSomatic
calculateTangentNormal	calculateTangentNormal
callAlterations	callAlterations
callAlterationsFromSegmentation	callAlterationsFromSegmentation
callAmplificationsInLowPurity	callAmplificationsInLowPurity
callCIN	callCIN
callLOH	callLOH
callMutationBurden	callMutationBurden
centromeres	centromeres
correctCoverageBias	correctCoverageBias
createCurationFile	createCurationFile
createNormalDatabase	createNormalDatabase
filterIntervals	filterIntervals
filterVcfBasic	filterVcfBasic
filterVcfMuTect	filterVcfMuTect
filterVcfMuTect2	filterVcfMuTect2
findFocal	findFocal
getSexFromCoverage	getSexFromCoverage
getSexFromVcf	getSexFromVcf
plotAbs	plotAbs
poolCoverage	poolCoverage
predictSomatic	predictSomatic
preprocessIntervals	preprocessIntervals
processMultipleSamples	processMultipleSamples
PureCN-defunct	PureCN-defunct
PureCN-deprecated	PureCN-deprecated
purecn.DNAcopy.bdry	purecn.DNAcopy.bdry
purecn.example.output	purecn.example.output
readAllelicCountsFile	readAllelicCountsFile
readCoverageFile	readCoverageFile
readCurationFile	readCurationFile
readIntervalFile	readIntervalFile
readLogRatioFile	readLogRatioFile
readSegmentationFile	readSegmentationFile
runAbsoluteCN	runAbsoluteCN
segmentationCBS	segmentationCBS
segmentationGATK4	segmentationGATK4
segmentationHclust	segmentationHclust
segmentationPSCBS	segmentationPSCBS
setMappingBiasVcf	setMappingBiasVcf
setPriorVcf	setPriorVcf
