annotateTargets	annotateTargets
autoCurateResults	autoCurateResults
bootstrapResults	bootstrapResults
calculateBamCoverageByInterval	calculateBamCoverageByInterval
calculateGCContentByInterval	calculateGCContentByInterval
calculateLogRatio	calculateLogRatio
calculatePowerDetectSomatic	calculatePowerDetectSomatic
callAlterations	callAlterations
callAlterationsFromSegmentation	callAlterationsFromSegmentation
callLOH	callLOH
callMutationBurden	callMutationBurden
centromeres	centromeres
correctCoverageBias	correctCoverageBias
createCurationFile	createCurationFile
createNormalDatabase	createNormalDatabase
createSNPBlacklist	createSNPBlacklist
createTargetWeights	createTargetWeights
filterTargets	filterTargets
filterVcfBasic	filterVcfBasic
filterVcfMuTect	filterVcfMuTect
filterVcfMuTect2	filterVcfMuTect2
findBestNormal	findBestNormal
findFocal	findFocal
getDiploid	getDiploid
getSexFromCoverage	getSexFromCoverage
getSexFromVcf	getSexFromVcf
plotAbs	plotAbs
plotBestNormal	plotBestNormal
poolCoverage	poolCoverage
predictSomatic	predictSomatic
PureCN-defunct	PureCN-defunct
PureCN-deprecated	PureCN-deprecated
purecn.example.output	purecn.example.output
readCoverageFile	readCoverageFile
readCoverageGatk	readCoverageGatk
readCurationFile	readCurationFile
runAbsoluteCN	runAbsoluteCN
segmentationCBS	segmentationCBS
segmentationPSCBS	segmentationPSCBS
setMappingBiasVcf	setMappingBiasVcf
setPriorVcf	setPriorVcf
