T
Bases
TakeLociIterator
set
TissueType
Input
TooManyCallsAtSite
annotation
Trigger
SomaticGenotypePolicy
TruncatedToString
strings
Tumor
TissueType
TumorDNASingleSampleSingleAlleleEvidence
evidence
TumorNormalReadsArgs
args
TumorRNASingleSampleSingleAlleleEvidence
evidence
take
LociSet
tissueType
Input
tissueTypes
Arguments
toBDGGenotype
CalledAllele
CalledSomaticAllele
ReferenceVariant
toCigar
ReadAlignment
toCigarString
ReadAlignment
toCoverageRDD
CoverageRDD
toHtsJDKIntervals
LociSet
toSeq
MultiSampleAnnotations
SingleSampleAnnotations
toString
AlleleCount
Input
Coverage
LociPartitioning
MappedRead
Position
TruncatedToString
Allele
Genotype
topAlt
PileupStats
totalDepthIncludingReadsContributingNoAlleles
PileupStats
totalForward
StrandBias
totalReads
InsufficientNormal
totalReverse
StrandBias
transform
AlleleAtLocus
trimRanges
CappedRegionsPartitionerArgs
truncatedAllelicDepths
PileupStats
truncatedString
TruncatedToString
truthGenotypesFile
ConcordanceArgs
tryCompareTo
Position
tumor
Input
tumorDNA
Input
InputCollection
tumorDNAPooled
MultiplePileupStats
tumorDNAPooledEvidence
MultiSampleSingleAlleleEvidence
tumorDNAPooledIndex
MultiSampleSingleAlleleEvidence
tumorDnaSampleIndicesTriggered
MultiSampleSingleAlleleEvidence
tumorRNA
Input
InputCollection
tumorReads
TumorNormalReadsArgs
tumorRnaSampleExpressed
MultiSampleSingleAlleleEvidence
tumorSampleName
TumorNormalReadsArgs
tumorVariantEvidence
CalledSomaticAllele