A
Bases
ALT
Bases
AffineGapPenaltyAlignment
alignment
AlignmentState
alignment AlignmentState
All
parsing
AllRange
parsing
Allele
variants
AlleleAtLocus
jointcaller
AlleleCount
Caller
AlleleEvidence
variants
AlleleMixture
PileupStats
AlleleSerializer
variants
Analyte
Input
Annotation
MultiSampleAnnotations SingleSampleAnnotations
Args
commands
Arguments
GermlineAssemblyCaller SomaticJoint SomaticStandard VAFHistogram VariantSupport InputCollection args
ArrayBackedReferenceSequence
ReferenceBroadcast
AssemblyArgs
assembly
AssemblyUtils
assembly
AverageBaseQualityFilter
genotype
AverageMappingQualityFilter
genotype
addInfoToVCF
MultiSampleAnnotations Annotation SingleSampleAnnotations Annotation StrandBias
addVCFHeaders
InsufficientNormal MultiSampleAnnotations SingleSampleAnnotations StrandBias TooManyCallsAtSite
advanceMultipleWindows
SlidingWindow
advanceToLocus
PileupElement
advanceToNextCigarElement
PileupElement
align
AffineGapPenaltyAlignment
alignment
guacamole PileupElement
alignmentLikelihood
MappedRead
alignmentQuality
MappedRead
alignmentScore
ReadAlignment
alignments
ReadAlignment
all
ParsedLoci LociSet
allEvidences
MultiSampleSingleAlleleEvidence
allMappedReads
ReadSets
allStandardBases
Bases
allele
MultiSampleSingleAlleleEvidence NormalDNASingleSampleSingleAlleleEvidence SingleSampleSingleAlleleEvidence TumorDNASingleSampleSingleAlleleEvidence TumorRNASingleSampleSingleAlleleEvidence PileupElement CalledAllele CalledSomaticAllele ReferenceVariant
alleleForwardDepth
AlleleEvidence
alleleMixture
Genotype
alleleReadDepth
AlleleEvidence
alleleReadDepthAndPositiveDepth
Pileup
alleleSerializer
HasAlleleSerializer
alleleToSubsequences
PileupStats
alleles
Genotype
allelesToMixture
NormalDNASingleSampleSingleAlleleEvidence
allelicDepths
NormalDNASingleSampleSingleAlleleEvidence TumorDNASingleSampleSingleAlleleEvidence TumorRNASingleSampleSingleAlleleEvidence PileupStats
alt
AlleleAtLocus
altBases
Allele
alternate
AlleleCount
analyte
Input
analytes
Arguments
annotate
MultiSampleSingleAlleleEvidence
annotation
jointcaller
annotations
MultiSampleSingleAlleleEvidence NormalDNASingleSampleSingleAlleleEvidence SingleSampleSingleAlleleEvidence TumorDNASingleSampleSingleAlleleEvidence TumorRNASingleSampleSingleAlleleEvidence
annotationsFailingFilters
MultiSampleAnnotations SingleSampleAnnotations
anyAlleleMinSupportingPercent
Parameters CommandlineArguments
anyAlleleMinSupportingReads
Parameters CommandlineArguments
apply
DeBruijnGraph VariantLocus FishersExactTest AverageBaseQualityFilter AverageMappingQualityFilter GenotypeFilter MinimumAlternateReadDepthFilter MinimumLikelihoodFilter ReadDepthFilter SomaticAlternateReadDepthFilter SomaticAverageBaseQualityFilter SomaticAverageMappingQualityFilter SomaticGenotypeFilter SomaticLogOddsFilter SomaticMedianMismatchFilter SomaticMinimumLikelihoodFilter SomaticReadDepthFilter SomaticVAFFilter InputCollection Parameters InsufficientNormal MultiSampleAnnotations SingleSampleAnnotations StrandBias TooManyCallsAtSite MultiSampleSingleAlleleEvidence NormalDNASingleSampleSingleAlleleEvidence TumorDNASingleSampleSingleAlleleEvidence TumorRNASingleSampleSingleAlleleEvidence PileupStats Contig LociMap LociRange ParsedLoci ParsedLociRange ParsedLociRanges LociPartitioning LociSet DelayedMessages Deletion Pileup PileupElement MateAlignmentProperties Read ReadSets Input ContigsIterator PartitionedRegions ContigIterator ContigSequence Interval Position ReferenceBroadcast ArrayBackedReferenceSequence MapBackedReferenceSequence ReferenceRegion TruncatedToString Allele AlleleEvidence
args
loci readsets
asLog
FishersExactTest
asLog10
FishersExactTest
asMap
Contig
asMappedRead
MappedRead PairedRead Read UnmappedRead
asStringPairs
Parameters
assembly
guacamole
assemblyWindowRange
AssemblyArgs
assertAllStandardBases
Bases
assertStandardBase
Bases
atGreaterLocus
Pileup
availableContigs
ContigNotFound