N
Bases
NoSequenceDictionaryArgs
args
Normal
TissueType
NormalDNASingleSampleSingleAlleleEvidence
evidence
NumLoci
reference
NumMicroPartitions
MicroRegionPartitioner
NumPartitions
LociPartitioner
NumSamples
readsets
name
Command
Caller
PartitionLoci
PartitionReads
Caller
Caller
Caller
Caller
InsufficientNormal
Annotation
Annotation
StrandBias
TooManyCallsAtSite
Contig
Contig
MappedRead
PairedRead
Read
UnmappedRead
newBuilder
LociMap
newRegions
SlidingWindow
next
RegionsByContig
SingleContigRegionIterator
ContigIterator
nextAlts
ReadSubsequence
nextCigarElement
PileupElement
nextLocusWithRegions
SlidingWindow
noSequenceDictionary
NoSequenceDictionaryArgs
nonDuplicate
InputFilters
nonEmpty
Contig
LociSet
nonRefAlleles
PileupStats
normal
Input
normalDNA
Input
InputCollection
normalDNAPooled
MultiplePileupStats
normalDNAPooledEvidence
MultiSampleSingleAlleleEvidence
normalDNAPooledIndex
MultiSampleSingleAlleleEvidence
normalRNA
Input
InputCollection
normalReads
TumorNormalReadsArgs
normalReferenceEvidence
CalledSomaticAllele
normalSampleName
TumorNormalReadsArgs
numCalls
TooManyCallsAtSite
numClusters
Arguments
numLoci
PartitionedRegions
numPartitions
LociPartitioning
UniformMicroPartitioner
UniformPartitioner
UniformPartitionerArgs
numSamples
ReadSets
numberOfVariantAlleles
Genotype