All Classes
AbstractAlignmentMerger
AbstractAlignmentMerger
AbstractAlignmentMerger.UnmappingReadStrategy
AbstractConcordanceWalker
AbstractConcordanceWalker.TruthVersusEval
AbstractIlluminaPositionFileReader
AbstractInputParser
AbstractLocatableCollection
AbstractMarkDuplicatesCommandLineProgram
AbstractMarkDuplicatesCommandLineProgram
AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
AbstractOpticalDuplicateFinderCommandLineProgram
AbstractOpticalDuplicateFinderCommandLineProgram
AbstractRecordCollection
AbstractSampleLocatableCollection
AbstractSampleRecordCollection
AbstractWgsMetricsCollector
AccumulateVariantCallingMetrics
ActivityProfile
ActivityProfileState
ActivityProfileState.Type
AdapterMarker
AdapterPair
AdapterPair
AdapterTrimTransformer
AdapterUtility
AdaptiveMetropolisSampler
AddCommentsToBam
AddContextDataToReadSpark
AddContextDataToReadSparkOptimized
AddContextDataToReadSparkOptimized.SubdivideAndFillReadsIterator
AddOrReplaceReadGroups
AFCalculationResult
AFCalculator
AFCalculatorImplementation
AFCalculatorProvider
Affection
AFPriorProvider
AggregatedSubHaplotypeFinder
AlignedAssembly
AlignedAssembly.Serializer
AlignedAssemblyOrExcuse
AlignedAssemblyOrExcuse.Serializer
AlignedContig
AlignedContig.Serializer
AlignedContigGenerator
AlignmentAgreesWithHeaderReadFilter
AlignmentContext
AlignmentContext.ReadOrientation
AlignmentContextIteratorBuilder
AlignmentInterval
AlignmentInterval.Serializer
AlignmentStateMachine
AlignmentSummaryMetrics
AlignmentSummaryMetrics.Category
AlignmentSummaryMetricsCollector
AlignmentUtils
AlignmentUtils.MismatchCount
AlleleBalanceFilter
AlleleBiasedDownsamplingUtils
AlleleFractionKernelSegmenter
AlleleFractionModeller
AlleleFractionParameter
AlleleFractionPrior
AlleleFractionSegment
AlleleFractionSegmentCollection
AlleleFrequencyCalculator
AlleleLikelihoodMatrixMapper
AlleleList
AlleleList.ActualPermutation
AlleleList.NonPermutation
AlleleListPermutation
AllelePileupCounter
AlleleSpecificAnnotationData
AlleleSubsettingUtils
AlleleSubsettingUtils
AllelicCount
AllelicCountCollection
AllelicCountCollector
AllLocusIterator
AmbiguousBaseReadFilter
AminoAcid
AnalyzeCovariates
AnnotatedInterval
AnnotatedInterval
AnnotatedIntervalCodec
AnnotatedIntervalCollection
AnnotatedIntervalCollection
AnnotatedIntervalHeader
AnnotatedIntervalUtils
AnnotatedIntervalWriter
AnnotatedVariantProducer
AnnotateIntervals
AnnotatePairOrientation
AnnotateVcfWithBamDepth
AnnotateVcfWithExpectedAlleleFraction
Annotation
AnnotationException
AnnotationSet
AnnotationUtils
ApacheSingularValueDecomposer
ApplyBQSR
ApplyBQSRArgumentCollection
ApplyBQSRSpark
ApplyBQSRSparkFn
ApplyBQSRUniqueArgumentCollection
ApplyVQSR
ArgumentsBuilder
ArtifactStatisticsScorer
ArtificialBAMBuilder
ArtificialReadIterator
ArtificialReadQueryIterator
ArtificialReadUtils
AS_BaseQualityRankSumTest
AS_FisherStrand
AS_InbreedingCoeff
AS_MappingQualityRankSumTest
AS_QualByDepth
AS_RankSumTest
AS_ReadPosRankSumTest
AS_RMSMappingQuality
AS_StandardAnnotation
AS_StrandBiasTest
AS_StrandOddsRatio
ASEReadCounter
ASEReadCounter.CountPileupType
ASEReadCounter.OUTPUT_FORMAT
AssemblyBasedCallerArgumentCollection
AssemblyBasedCallerGenotypingEngine
AssemblyBasedCallerGenotypingEngine.CalledHaplotypes
AssemblyBasedCallerUtils
AssemblyContigAlignmentsConfigPicker
AssemblyContigAlignmentsConfigPicker.GoodAndBadMappings
AssemblyContigWithFineTunedAlignments
AssemblyContigWithFineTunedAlignments.AlignmentSignatureBasicType
AssemblyContigWithFineTunedAlignments.ReasonForAlignmentClassificationFailure
AssemblyContigWithFineTunedAlignments.Serializer
AssemblyRegion
AssemblyRegionEvaluator
AssemblyRegionIterator
AssemblyRegionTrimmer
AssemblyRegionTrimmer.Result
AssemblyRegionTrimmerArgumentCollection
AssemblyRegionWalker
AssemblyRegionWalkerContext
AssemblyRegionWalkerSpark
AssemblyResult
AssemblyResult.Status
AssemblyResultSet
AsynchronousStreamWriterService
AsyncIterator
AtomicIterator
BaitDesigner
BaitDesigner.DesignStrategy
BamIndexStats
BamToBfq
BamToBfqWriter
BandPassActivityProfile
BAQ
BAQ.BAQCalculationResult
BAQ.CalculationMode
BAQ.QualityMode
BarcodeFileFaker
BarcodeFileReader
BaseBclReader
BaseCallingProgramGroup
BaseDistributionByCycleMetrics
BaseDistributionByCycleMetrics
BaseEdge
BaseGraph
BaseIlluminaDataProvider
BaselineCopyNumberCollection
BaseQuality
BaseQualityClipReadTransformer
BaseQualityRankSumTest
BaseQualityReadTransformer
BaseRecalibrationEngine
BaseRecalibrationEngine.BQSRReferenceWindowFunction
BaseRecalibrator
BaseRecalibratorEngineSparkWrapper
BaseRecalibratorSpark
BaseRecalibratorSparkFn
BaseRecalibratorSparkSharded
BaseTest
BaseTest.TestDataProvider
BaseUtils
BaseUtils.Base
BaseUtils.BaseSubstitutionType
BaseVertex
BasicInputParser
BasicSomaticShortMutationValidator
BasicValidationResult
BciFileFaker
BclData
BclFileFaker
BclIndexReader
BclQualityEvaluationStrategy
BclReader
BDGAlignmentRecordToGATKReadAdapter
BedToIntervalList
BestEndMapqPrimaryAlignmentStrategy
BestEndMapqPrimaryAlignmentStrategy
BestMapqPrimaryAlignmentSelectionStrategy
BestMapqPrimaryAlignmentSelectionStrategy
BetaBinomialDistribution
BQSRPipelineSpark
BQSRReadTransformer
BreakEndVariantType
BreakEndVariantType.InvSuspectBND
BreakEndVariantType.TransLocBND
BreakpointComplications
BreakpointComplications.IntraChrStrandSwitchBreakpointComplications
BreakpointComplications.IntraChrStrandSwitchBreakpointComplications.Serializer
BreakpointComplications.SmallDuplicationWithImpreciseDupRangeBreakpointComplications
BreakpointComplications.SmallDuplicationWithImpreciseDupRangeBreakpointComplications.Serializer
BreakpointComplications.SmallDuplicationWithPreciseDupRangeBreakpointComplications
BreakpointComplications.SmallDuplicationWithPreciseDupRangeBreakpointComplications.Serializer
BreakpointDensityFilter
BreakpointEvidence
BreakpointEvidence.DiscordantReadPairEvidence
BreakpointEvidence.ExternalEvidence
BreakpointEvidence.ExternalEvidence.Serializer
BreakpointEvidence.InterContigPair
BreakpointEvidence.InterContigPair.Serializer
BreakpointEvidence.LargeIndel
BreakpointEvidence.LargeIndel.Serializer
BreakpointEvidence.MateUnmapped
BreakpointEvidence.MateUnmapped.Serializer
BreakpointEvidence.OutiesPair
BreakpointEvidence.OutiesPair.Serializer
BreakpointEvidence.ReadEvidence
BreakpointEvidence.ReadEvidence.Serializer
BreakpointEvidence.SameStrandPair
BreakpointEvidence.SameStrandPair.Serializer
BreakpointEvidence.Serializer
BreakpointEvidence.SplitRead
BreakpointEvidence.SplitRead.Serializer
BreakpointEvidence.TemplateSizeAnomaly
BreakpointEvidence.TemplateSizeAnomaly.Serializer
BreakpointEvidence.WeirdTemplateSize
BreakpointEvidence.WeirdTemplateSize.Serializer
BreakpointEvidenceClusterer
BroadcastJoinReadsWithRefBases
BroadcastJoinReadsWithVariants
BucketUtils
BuildBamIndex
BunnyLog
BwaAndMarkDuplicatesPipelineSpark
BwaArgumentCollection
BwaMemAlignmentUtils
BwaMemIndexCache
BwaMemIndexImageCreator
BwaSpark
BwaSparkEngine
ByIntervalListVariantContextIterator
ByteArrayIterator
CachingIndexedFastaSequenceFile
CalcMetadataSpark
CalculateContamination
CalculateGenotypePosteriors
CalculateMixingFractions
CalculateReadGroupChecksum
CallCopyRatioSegments
CalledCopyRatioSegment
CalledCopyRatioSegment.Call
CalledCopyRatioSegmentCollection
CallingMetricAccumulator
CallingMetricAccumulator.Result
CapturedStreamOutput
CapturedStreamOutputSnapshot
Casava18ReadNameEncoder
CbclData
CbclReader
ChannelAsSeekableStream
CheckFingerprint
CheckIlluminaDirectory
CheckPileup
CheckTerminatorBlock
ChimeraUtil
ChromosomeCounts
CigarUtils
CircularByteBuffer
ClassFinder
ClassUtils
CleanSam
CleanSamTester
ClippingOp
ClippingRankSumTest
ClippingRepresentation
ClippingUtility
ClipReads
ClipReads.ClippingData
ClipReads.ReadClipperWithData
ClocsFileFaker
ClocsFileReader
ClusterCrosscheckMetrics
ClusterData
ClusterDataToSamConverter
ClusteredCrosscheckMetric
CNNScoreVariants
CNNVariantTrain
CNNVariantWriteTensors
CNVInputReader
CollectAlignmentSummaryMetrics
CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection
CollectAllelicCounts
CollectBaseDistributionByCycle
CollectBaseDistributionByCycleSpark
CollectGcBiasMetrics
CollectHiSeqXPfFailMetrics
CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
CollectHiSeqXPfFailMetrics.ReadClassifier
CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
CollectHsMetrics
CollectIlluminaBasecallingMetrics
CollectIlluminaLaneMetrics
CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
CollectIndependentReplicateMetrics
CollectInsertSizeMetrics
CollectInsertSizeMetricsSpark
CollectJumpingLibraryMetrics
CollectMultipleMetrics
CollectMultipleMetrics.Program
CollectMultipleMetrics.ProgramInterface
CollectMultipleMetricsSpark
CollectMultipleMetricsSpark.SparkCollectorProvider
CollectMultipleMetricsSpark.SparkCollectors
CollectOxoGMetrics
CollectOxoGMetrics.CpcgMetrics
CollectQualityYieldMetrics
CollectQualityYieldMetrics.QualityYieldMetrics
CollectQualityYieldMetrics.QualityYieldMetricsCollector
CollectQualityYieldMetricsSpark
CollectRawWgsMetrics
CollectRawWgsMetrics.RawWgsMetrics
CollectReadCounts
CollectRnaSeqMetrics
CollectRrbsMetrics
CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection
CollectSequencingArtifactMetrics
CollectTargetedMetrics
CollectTargetedPcrMetrics
CollectVariantCallingMetrics
CollectVariantCallingMetrics.VariantCallingDetailMetrics
CollectVariantCallingMetrics.VariantCallingSummaryMetrics
CollectWgsMetrics
CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection
CollectWgsMetrics.WgsMetrics
CollectWgsMetrics.WgsMetricsCollector
CollectWgsMetricsWithNonZeroCoverage
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
CombineGVCFs
CombineSegmentBreakpoints
CommandLineDefaults
CommandLineProgram
CommandLineProgram
CommandLineProgramTester
CommandLineSyntaxTranslater
CommonSuffixSplitter
CompareBaseQualities
CompareDuplicatesSpark
CompareMatrix
CompareMetrics
CompareSAMs
ComplexityPartitioner
CompressedDataList
Concordance
ConcordanceState
ConcordanceSummaryRecord
ConcordanceSummaryRecord.Reader
ConcordanceSummaryRecord.Writer
ConcurrentAFCalculatorProvider
ConfigFactory
ContainsKmerReadFilter
ContainsKmerReadFilterSpark
ContaminationRecord
ContaminationRecord.Level
ContextCovariate
ContextShard
ContigAlignmentsModifier
ContigAlignmentsModifier.AlnModType
ContigAlignmentsModifier.AlnModType.ModTypeString
ConvertHeaderlessHadoopBamShardToBam
ConvertSequencingArtifactToOxoG
CopyNumberArgumentValidationUtils
CopyNumberFormatsUtils
CopyNumberPosteriorDistribution
CopyNumberPosteriorDistributionCollection
CopyNumberProgramGroup
CopyNumberStandardArgument
CopyRatio
CopyRatioCollection
CopyRatioKernelSegmenter
CopyRatioModeller
CopyRatioParameter
CopyRatioSegment
CopyRatioSegmentCollection
CosmicFuncotationFactory
CountBases
CountBasesSpark
CounterManager
CountFalsePositives
CountingDuplicateFilter
CountingFilter
CountingMapQFilter
CountingPairedFilter
CountingReadFilter
CountingReadFilter.CountingAndReadFilter
CountingVariantFilter
CountingVariantFilter.CountingAndVariantFilter
CountReads
CountReadsSpark
CountSet
CountVariants
CountVariantsSpark
Covariate
CovariateKeyCache
Coverage
CoverageAnalysisProgramGroup
CoveragePerContig
CoveragePerContigCollection
CpxVariantInterpreter
CpxVariantReInterpreterSpark
CreateHadoopBamSplittingIndex
CreateReadCountPanelOfNormals
CreateSequenceDictionary
CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection
CreateSomaticPanelOfNormals
CreateSomaticPanelOfNormals.DuplicateSampleStrategy
CrosscheckFingerprints
CrosscheckMetric
CrosscheckMetric.DataType
CrosscheckMetric.FingerprintResult
CrosscheckReadGroupFingerprints
CsvInputParser
CustomAFPriorProvider
CustomBooleanConverter
CycleCovariate
DataCollection
DataLine
DataSourceFuncotationFactory
DataSourceUtils
DbsnpArgumentCollection
DbSnpBitSetUtil
DbSnpBitSetUtil
DbSnpBitSetUtil.DbSnpBitSets
DbSnpBitSetUtil.DbSnpBitSets
DbSnpVariantType
Decile
DecileCollection
DefaultGATKReadFilterArgumentCollection
DefaultGATKVariantAnnotationArgumentCollection
DelimitedTextFileWithHeaderIterator
DenoiseReadCounts
DeprecatedToolsRegistry
DepthFilter
DepthPerAlleleBySample
DepthPerSampleHC
DetermineGermlineContigPloidy
DetermineGermlineContigPloidy.RunMode
DiagnosticsAndQCProgramGroup
DiploidGenotype
DiploidGenotype
DiploidHaplotype
Dirichlet
DiscoverVariantsFromContigAlignmentsSAMSpark
DiskBasedReadEndsForMarkDuplicatesMap
DiskBasedReadEndsForMarkDuplicatesMap
DoNotSubclass
DownsampleableSparkReadShard
Downsampler
DownsampleSam
DownsampleType
DownsamplingMethod
DuplicationMetrics
DUSTReadTransformer
EarliestFragmentPrimaryAlignmentSelectionStrategy
EarliestFragmentPrimaryAlignmentSelectionStrategy
EmpiricalPhasingMetricsOutReader
EmpiricalPhasingMetricsOutReader.IlluminaPhasingMetrics
EmptyFragment
ErrorSummaryMetrics
EstimateLibraryComplexity
EstimateLibraryComplexityGATK
EventMap
EventType
EvidenceTargetLink
EvidenceTargetLink.Serializer
EvidenceTargetLinkClusterer
ExactACcounts
ExactACset
ExampleAssemblyRegionWalker
ExampleAssemblyRegionWalkerSpark
ExampleCollectMultiMetricsSpark
ExampleCollectSingleMetricsSpark
ExampleFeatureWalker
ExampleIntervalWalker
ExampleIntervalWalkerSpark
ExampleLocusWalker
ExampleMultiMetrics
ExampleMultiMetricsArgumentCollection
ExampleMultiMetricsCollector
ExampleMultiMetricsCollectorSpark
ExampleNioCountReads
ExamplePostTraversalPythonExecutor
ExampleProgramGroup
ExampleReadWalkerWithReference
ExampleReadWalkerWithReferenceSpark
ExampleReadWalkerWithVariants
ExampleSingleMetrics
ExampleSingleMetricsArgumentCollection
ExampleSingleMetricsCollectorSpark
ExampleStreamingPythonExecutor
ExampleTwoPassVariantWalker
ExampleVariantWalker
ExampleVariantWalkerSpark
ExcessHet
ExomeStandardArgumentDefinitions
ExpandingArrayList
ExtractIlluminaBarcodes
ExtractIlluminaBarcodes.BarcodeMetric
ExtractIlluminaBarcodes.PerTileBarcodeExtractor
ExtractIlluminaBarcodes.PerTileBarcodeExtractor.BarcodeMatch
ExtractOriginalAlignmentRecordsByNameSpark
ExtractSequences
ExtractSVEvidenceSpark
FakeReferenceSource
FalsePositiveRecord
FamilyLikelihoods
FastaReferenceWriter
FastqToSam
FastWgsMetricsCollector
FeatureContext
FeatureDataSource
FeatureInput
FeatureManager
FeatureWalker
FermiLiteAssemblyHandler
FifoBuffer
FileFaker
FilterAlignmentArtifacts
FilterAnalysisRecord
FilterApplyingVariantIterator
FilterByOrientationBias
FilterFileFaker
FilterFileReader
FilterMutectCalls
FilterSamReads
FilterSamReads.Filter
FilterVariantTranches
FilterVcf
FindBadGenomicKmersSpark
FindBreakpointEvidenceSpark
FindBreakpointEvidenceSpark.AssembledEvidenceResults
FindBreakpointEvidenceSpark.IntPair
FindMendelianViolations
Fingerprint
FingerprintChecker
FingerprintIdDetails
FingerprintingDetailMetrics
FingerprintingSummaryMetrics
FingerprintResults
FingerprintUtils
FingerprintUtils.VariantContextSet
FisherExactTest
FisherStrand
FisherStrandFilter
FixCallSetSampleOrdering
FixedAFCalculatorProvider
FixMateInformation
FixMisencodedBaseQualityReads
FixVcfHeader
FlagStat
FlagStat.FlagStatus
FlagStatSpark
FlatMapGluer
ForwardBackwardAlgorithm
ForwardBackwardAlgorithm.Result
FourChannelIntensityData
FractionalDownsampler
Fragment
FragmentCollection
FragmentLength
FragmentLengthReadFilter
FragmentUtils
Funcotation
Funcotator
FuncotatorArgumentDefinitions
FuncotatorArgumentDefinitions.DataSourceType
FuncotatorArgumentDefinitions.OutputFormatType
FuncotatorUtils
FuncotatorUtils.TranscriptCodingSequenceException
GA4GHScheme
GA4GHSchemeWithMissingAsHomRef
GatherBamFiles
GatherBQSRReports
GatherTranches
GatherVcfs
GatherVcfsCloud
GatherVcfsCloud.GatherType
GATKAnnotationArgumentCollection
GATKAnnotationPluginDescriptor
GATKConfig
GATKDataSource
GATKDocWorkUnit
GATKDuplicationMetrics
GATKException
GATKException.MissingReadField
GATKException.ReadAttributeTypeMismatch
GATKException.ShouldNeverReachHereException
GATKGSONWorkUnit
GATKHelpDoclet
GATKHelpDocWorkUnitHandler
GATKProtectedVariantContextUtils
GATKRead
GATKReadFilterArgumentCollection
GATKReadFilterPluginDescriptor
GATKReadToBDGAlignmentRecordConverter
GATKReadWriter
GATKRegistrator
GATKReport
GATKReportColumn
GATKReportColumnFormat
GATKReportColumnFormat.Alignment
GATKReportDataType
GATKReportTable
GATKReportTable.Sorting
GATKReportTable.TableDataHeaderFields
GATKReportTable.TableNameHeaderFields
GATKReportVersion
GATKSparkTool
GATKSVVCFConstants
GATKSVVCFHeaderLines
GATKTool
GATKVariant
GATKVariantContextUtils
GATKVariantContextUtils.AlleleMapper
GATKVariantContextUtils.FilteredRecordMergeType
GATKVariantContextUtils.GenotypeMergeType
GATKVCFConstants
GATKVCFHeaderLines
GATKVCFIndexType
GCBiasCorrector
GcBiasDetailMetrics
GcBiasMetrics
GcBiasMetricsCollector
GcBiasSummaryMetrics
GcBiasUtils
GencodeFuncotation
GencodeFuncotation.VariantClassification
GencodeFuncotation.VariantType
GencodeFuncotationBuilder
GencodeFuncotationFactory
GencodeGtfCDSFeature
GencodeGtfCodec
GencodeGtfExonFeature
GencodeGtfFeature
GencodeGtfFeature.AnnotationSource
GencodeGtfFeature.FeatureTag
GencodeGtfFeature.FeatureType
GencodeGtfFeature.GeneTranscriptStatus
GencodeGtfFeature.GeneTranscriptType
GencodeGtfFeature.GenomicPhase
GencodeGtfFeature.LocusLevel
GencodeGtfFeature.OptionalField
GencodeGtfFeature.RemapStatus
GencodeGtfFeature.RemapTargetStatus
GencodeGtfFeature.TranscriptSupportLevel
GencodeGtfFeatureBaseData
GencodeGtfGeneFeature
GencodeGtfSelenocysteineFeature
GencodeGtfStartCodonFeature
GencodeGtfStopCodonFeature
GencodeGtfTranscriptFeature
GencodeGtfUTRFeature
Gene
GeneAnnotationReader
GeneralPloidyExactAFCalculator
GeneralPloidyFailOverAFCalculatorProvider
GenomeLoc
GenomeLocParser
GenomeLocParser.ValidationLevel
GenomeLocSortedSet
GenomicsDBConstants
GenomicsDBImport
GenomicsDBTestUtils
GenotypeAlleleCounts
GenotypeAnnotation
GenotypeAssignmentMethod
GenotypeCalculationArgumentCollection
GenotypeConcordance
GenotypeConcordance.Alleles
GenotypeConcordanceContingencyMetrics
GenotypeConcordanceCounts
GenotypeConcordanceDetailMetrics
GenotypeConcordanceScheme
GenotypeConcordanceSchemeFactory
GenotypeConcordanceStateCodes
GenotypeConcordanceStates
GenotypeConcordanceStates.CallState
GenotypeConcordanceStates.ContingencyState
GenotypeConcordanceStates.TruthAndCallStates
GenotypeConcordanceStates.TruthState
GenotypeConcordanceSummaryMetrics
GenotypeCounts
GenotypeFilter
GenotypeGVCFs
GenotypeLikelihoodCalculator
GenotypeLikelihoodCalculators
GenotypeLikelihoodsCalculationModel
GenotypeQualityFilter
GenotypeSummaries
GenotypeUtils
GenotypingData
GenotypingEngine
GenotypingGivenAllelesUtils
GenotypingLikelihoods
GenotypingOutputMode
GermlineCallingArgumentCollection
GermlineCNVCaller
GermlineCNVCaller.RunMode
GermlineCNVHybridADVIArgumentCollection
GermlineCNVIntervalVariantComposer
GermlineCNVNamingConstants
GermlineCNVSegmentVariantComposer
GermlineCNVVariantComposer
GermlineContigPloidyHybridADVIArgumentCollection
GermlineContigPloidyModelArgumentCollection
GermlineDenoisingModelArgumentCollection
GermlineDenoisingModelArgumentCollection.CopyNumberPosteriorExpectationMode
GermlineProbabilityCalculator
GetPileupSummaries
GetSampleName
GibbsSampler
GraphUtils
GraphUtils
GraphUtils.Graph
GvcfMetricAccumulator
GVCFWriter
Haplotype
HaplotypeBAMDestination
HaplotypeBAMWriter
HaplotypeBAMWriter.WriterType
HaplotypeBlock
HaplotypeCaller
HaplotypeCallerArgumentCollection
HaplotypeCallerEngine
HaplotypeCallerGenotypingEngine
HaplotypeCallerSpark
HaplotypeCallerSpark.ReferenceMultiSourceAdapter
HaplotypeCallerSpark.ShardingArgumentCollection
HaplotypeMap
HaplotypeProbabilities
HaplotypeProbabilities.Genotype
HaplotypeProbabilitiesFromContaminatorSequence
HaplotypeProbabilitiesFromGenotype
HaplotypeProbabilitiesFromGenotypeLikelihoods
HaplotypeProbabilitiesFromSequence
HaplotypeProbabilityOfNormalGivenTumor
HardThresholdingOutputStream
HasGenomeLocation
HDF5SimpleCountCollection
HDF5SVDReadCountPanelOfNormals
HDF5Utils
HeaderlessSAMRecordCoordinateComparator
HelpConstants
HelpConstants
HeterogeneousPloidyModel
HeterozygosityAFPriorProvider
HeterozygosityCalculator
Histogram
HitsForInsert
HitsForInsert.NumPrimaryAlignmentState
HMM
HomogeneousPloidyModel
HomoSapiensConstants
HopscotchCollection
HopscotchCollection.Serializer
HopscotchMap
HopscotchMap.Serializer
HopscotchMultiMap
HopscotchMultiMap.Serializer
HopscotchSet
HopscotchSet.Serializer
HopscotchUniqueMultiMap
HopscotchUniqueMultiMap.Serializer
HostAlignmentReadFilter
HsMetricCollector
HsMetrics
HybridADVIArgumentCollection
HybridADVIArgumentCollection.HybridADVIArgument
IdentifyContaminant
IGVUtils
IlluminaAdapterPair
IlluminaBasecallingMetrics
IlluminaBasecallsConverter
IlluminaBasecallsToFastq
IlluminaBasecallsToFastq.ReadNameFormat
IlluminaBasecallsToSam
IlluminaDataProvider
IlluminaDataProviderFactory
IlluminaDataType
IlluminaFileUtil
IlluminaFileUtil.SupportedIlluminaFormat
IlluminaLaneMetrics
IlluminaMetricsCode
IlluminaPhasingMetrics
IlluminaReadNameEncoder
IlluminaUtil
IlluminaUtil.IlluminaAdapterPair
ImpreciseVariantDetector
InbreedingCoeff
IndependentAllelesDiploidExactAFCalculator
IndependentReplicateMetric
IndependentSampleGenotypesModel
IndexedAlleleList
IndexedSampleList
IndexedSet
IndexFeatureFile
IndexRange
IndexUtils
InfoFieldAnnotation
InputStreamSettings
InsertSizeMetrics
InsertSizeMetrics
InsertSizeMetricsArgumentCollection
InsertSizeMetricsCollector
InsertSizeMetricsCollector
InsertSizeMetricsCollectorSpark
IntBiConsumer
IntegerCopyNumberSegment
IntegerCopyNumberSegmentCollection
IntegerCopyNumberState
IntegrationTestSpec
IntegrationUtils
IntensityChannel
IntervalAlignmentContextIterator
IntervalArgumentCollection
IntervalArgumentCollection
IntervalCopyNumberGenotypingData
IntervalCoverageFinder
IntervalListScatterer
IntervalListScatterer.Mode
IntervalListToBed
IntervalListTools
IntervalListTools.Action
IntervalLocusIterator
IntervalMergingRule
IntervalOverlappingIterator
IntervalSetRule
IntervalsManipulationProgramGroup
IntervalsSkipList
IntervalsSkipListOneContig
IntervalUtils
IntervalUtils.IntervalBreakpointType
IntervalWalker
IntervalWalkerContext
IntervalWalkerSpark
IntHistogram
IntHistogram.CDF
IntHistogram.CDF.Serializer
IntHistogram.Serializer
IntToDoubleBiFunction
IOUtils
Iterators
JoinStrategy
JsonSerializer
JumpingLibraryMetrics
KBestHaplotype
KBestHaplotypeFinder
KernelSegmenter
KernelSegmenter.ChangepointSortOrder
Kmer
KmerAndCount
KmerAndCount.Serializer
KmerAndInterval
KmerAndInterval.Serializer
KmerCleaner
KmerCounter
KMerCounter
KmerSearchableGraph
KSWindowFinder
KV
LanePhasingMetricsCollector
LargeLongHopscotchSet
LargeLongHopscotchSet.Serializer
LeftAlignIndels
LevelingDownsampler
LibraryIdGenerator
LibraryIdGenerator
LibraryNameSplitter
LibraryReadFilter
LibraryStatistics
LibraryStatistics.Serializer
LIBSDownsamplingInfo
LiftOverIntervalList
LiftoverUtils
LiftoverVcf
LikelihoodEngineArgumentCollection
LikelihoodMatrix
LikelihoodRankSumTest
LineIteratorReader
LocatableMetadata
LocatableXsvFuncotationFactory
LocsFileFaker
LocsFileReader
LocusFunction
LocusIteratorByState
LocusWalker
LocusWalkerContext
LocusWalkerSpark
Log10PairHMM
LoggingUtils
LoglessPairHMM
LongBloomFilter
LongBloomFilter.Serializer
LongHopscotchSet
LongHopscotchSet.Serializer
LongIterator
LowWeightChainPruner
LRUCache
M2ArgumentCollection
M2FiltersArgumentCollection
MafOutputRenderer
Main
MakeSitesOnlyVcf
MannWhitneyU
MannWhitneyU.RankedData
MannWhitneyU.Result
MannWhitneyU.TestStatistic
MannWhitneyU.TestType
MappingQuality
MappingQualityRankSumTest
MappingQualityReadFilter
MappingQualityReadTransformer
MappingQualityZero
MarkDuplicates
MarkDuplicates.DuplicateTaggingPolicy
MarkDuplicates.DuplicateType
MarkDuplicatesGATK
MarkDuplicatesScoringStrategy
MarkDuplicatesSpark
MarkDuplicatesSparkArgumentCollection
MarkDuplicatesSparkRecord
MarkDuplicatesSparkRecord.Type
MarkDuplicatesSparkUtils
MarkDuplicatesSparkUtils.IndexPair
MarkDuplicatesSparkUtils.PairedEndsCoordinateComparator
MarkDuplicatesWithMateCigar
MarkDuplicatesWithMateCigarIterator
MarkedOpticalDuplicateReadFilter
MarkIlluminaAdapters
MarkQueue
MatchResults
MathUtil
MathUtil.LogMath
MathUtils
MathUtils.IntToDoubleArrayFunction
MathUtils.RunningAverage
MatrixSummaryUtils
MeanQualityByCycle
MeanQualityByCycleSpark
MendelianViolation
MendelianViolationMetrics
MendelianViolationsByFamily
MergeableMetricBase
MergeableMetricBase.MergeByAdding
MergeableMetricBase.MergeByAssertEquals
MergeableMetricBase.MergingIsManual
MergeableMetricBase.NoMergingIsDerived
MergeableMetricBase.NoMergingKeepsValue
MergeAnnotatedRegions
MergeBamAlignment
MergeSamFiles
MergeVcfs
Metadata
Metadata.Type
MetadataUtils
MetagenomicsProgramGroup
MetricAccumulationLevel
MetricAccumulationLevel
MetricAccumulationLevelArgumentCollection
MetricsArgumentCollection
MetricsCollectorSpark
MetricsCollectorSparkTool
MetricsReadFilter
MetricsUtils
MiniClusterUtils
MiniClusterUtils.MiniClusterTest
MinimalGenotypingEngine
MinimalVariant
MinorAlleleFractionRecord
MisencodedBaseQualityReadTransformer
MixingFraction
MMapBackedIteratorFactory
ModeledSegment
ModeledSegment.SimplePosteriorSummary
ModeledSegmentCollection
ModelSegments
MostDistantPrimaryAlignmentSelectionStrategy
MostDistantPrimaryAlignmentSelectionStrategy
MultiDeBruijnVertex
MultidimensionalKernelSegmenter
MultidimensionalModeller
MultidimensionalSegment
MultidimensionalSegmentCollection
MultiHitAlignedReadIterator
MultiIntervalLocalReadShard
MultiIntervalShard
MultiLevelCollector
MultiLevelCollector
MultiLevelMetrics
MultilevelMetrics
MultiLevelReducibleCollector
MultiSampleEdge
MultiTileBclFileFaker
MultiTileBclFileUtil
MultiTileBclParser
MultiTileFileUtil
MultiTileFilterParser
MultiTileLocsFileFaker
MultiTileLocsParser
MultiTileParser
MultiVariantDataSource
MultiVariantWalker
MultiVariantWalkerGroupedOnStart
Mutect2
Mutect2Engine
Mutect2FilteringEngine
MutectDownsampler
NativeUtils
NDNCigarReadTransformer
NestedIntegerArray
NestedIntegerArray.Leaf
NewIlluminaBasecallsConverter
NewIlluminaDataProvider
NGSPlatform
NioBam
NonChecksumLocalFileSystem
NonNFastaSize
NormalizeFasta
NotOpticalDuplicateReadFilter
NovelAdjacencyAndAltHaplotype
NovelAdjacencyAndAltHaplotype.Serializer
Nucleotide
Nucleotide.Counter
OjAlgoSingularValueDecomposer
OneShotLogger
OpticalDuplicateFinder
OpticalDuplicatesArgumentCollection
OptimizationUtils
OptionalFeatureInputArgumentCollection
OptionalIntervalArgumentCollection
OptionalReadInputArgumentCollection
OptionalReferenceArgumentCollection
OptionalReferenceInputArgumentCollection
OptionalVariantInputArgumentCollection
OrientationBiasFilterConstants
OrientationBiasFilterer
OrientationBiasFilterSummaryTableColumn
OrientationBiasUtils
OrientationSampleTransitionSummary
OtherProgramGroup
OutputMapping
OutputMode
OutputRenderer
OutputStreamSettings
OverclippedReadFilter
OverhangFixingManager
OxoGReadCounts
Pair
Pair.Serializer
PairedEnds
PairedStrandedIntervals
PairedStrandedIntervalTree
PairedStrandedIntervalTree.Serializer
PairedVariantSubContextIterator
PairedVariantSubContextIterator.VcfTuple
PairHMM
PairHMM.Implementation
PairHMMLikelihoodCalculationEngine
PairHMMLikelihoodCalculationEngine.PCRErrorModel
PairHMMModel
PairHMMNativeArgumentCollection
ParallelCopyGCSDirectoryIntoHDFSSpark
Parameter
ParameterDecileCollection
ParameterEnum
ParameterizedFileUtil
ParameterizedModel
ParameterizedModel.GibbsBuilder
ParameterizedModel.UpdateMethod
ParameterizedState
ParameterReader
ParameterSampler
ParameterTableColumn
ParameterWriter
ParamUtils
PartitionCrossingChecker
Passthrough
PassThroughDownsampler
Path
PathHelper
PathHelper.PathProviders
PathLineIterator
PathSeqBuildKmers
PathSeqBuildReferenceTaxonomy
PathSeqBwaSpark
PathSeqFilterSpark
PathSeqPipelineSpark
PathSeqScoreSpark
PedFile
PedigreeAnnotation
PedigreeValidationType
PedReader
PedReader.Field
PedReader.MissingPedField
PerAlleleAnnotation
PerAlleleCollection
PerAlleleCollection.Type
Permutation
PersistenceOptimizer
PerTileFileUtil
PerTileOrPerRunFileUtil
PerTileParser
PerTilePerCycleFileUtil
PerUnitExampleMultiMetricsCollector
PerUnitInsertSizeMetricsCollector
PerUnitMetricCollector
PerUnitMetricCollector
PGTagArgumentCollection
PhysicalLocation
PhysicalLocationForMateCigar
PhysicalLocationForMateCigarSet
PhysicalLocationInt
PhysicalLocationShort
PicardCommandLine
PicardCommandLineProgram
PicardCommandLineProgramExecutor
PicardException
PicardHelpDoclet
PicardHelpDocWorkUnitHandler
PicardNonZeroExitException
Pileup
PileupElement
PileupSpark
PileupSummary
PlatformReadFilter
PlatformUnitReadFilter
PloidyModel
PlotDenoisedCopyRatios
PlotModeledSegments
PosFileFaker
PosFileReader
PositionalDownsampler
PositionBasedDownsampleSam
PosParser
PossibleDeNovo
PosteriorProbabilitiesUtils
PosteriorProbabilitiesUtils.PosteriorProbabilitiesOptions
PosteriorSummary
PosteriorSummaryUtils
PostprocessGermlineCNVCalls
PowerCalculationUtils
PreAdapterOrientationScorer
PredicateFilterDecoratingClosableIterator
PreprocessIntervals
PrimaryAlignmentKey
PrimaryAlignmentSelectionStrategy
PrimaryAlignmentSelectionStrategy
PrintReads
PrintReadsSpark
PrintVariantsSpark
ProbabilityVector
ProcessController
ProcessControllerBase
ProcessControllerBase.ProcessStream
ProcessOutput
ProcessSettings
ProgressLogger
ProgressMeter
ProgressReportingDelegatingCodec
PropertyUtils
PSBuildReferenceTaxonomyUtils
PSBwaAligner
PSBwaAlignerSpark
PSBwaArgumentCollection
PSBwaFilter
PSBwaUtils
PSFilter
PSFilterArgumentCollection
PSFilterEmptyLogger
PSFilterFileLogger
PSFilterLogger
PSFilterMetrics
PSKmerBloomFilter
PSKmerBloomFilter.Serializer
PSKmerCollection
PSKmerSet
PSKmerSet.Serializer
PSKmerUtils
PSPairedUnpairedSplitterSpark
PSPathogenAlignmentHit
PSPathogenReferenceTaxonProperties
PSPathogenTaxonScore
PSScoreArgumentCollection
PSScoreFileLogger
PSScoreLogger
PSScoreMetrics
PSScorer
PSTaxonomyConstants
PSTaxonomyDatabase
PSTaxonomyDatabase.Serializer
PSTree
PSTree.Serializer
PSTreeNode
PSTreeNode.Serializer
PSUtils
PythonExecutorBase
PythonExecutorBase.PythonExecutableName
PythonScriptExecutor
PythonScriptExecutorException
QdFilter
QNameAndInterval
QNameAndInterval.Serializer
QNameFinder
QNameIntervalFinder
QNameKmerizer
QNamesForKmersFinder
QualByDepth
QualityScoreCovariate
QualityScoreDistribution
QualityScoreDistributionSpark
QualityUtils
QualityYieldMetrics
QualityYieldMetricsArgumentCollection
QualityYieldMetricsCollectorSpark
QualQuantizer
QuantizationInfo
QuerySortedReadPairIteratorUtil
QuerySortedReadPairIteratorUtil.ReadPair
RandomLikelihoodCalculationEngine
Range
RankSumTest
ReadCachingIterator
ReadClassifier
ReadClipper
ReadClipperTestUtils
ReadConstants
ReadContextData
ReadCoordinateComparator
ReadCovariates
ReadData
ReadDataManipulationProgramGroup
ReadDescriptor
ReadEnds
ReadEnds
ReadEndsForMarkDuplicates
ReadEndsForMarkDuplicates
ReadEndsForMarkDuplicatesCodec
ReadEndsForMarkDuplicatesCodec
ReadEndsForMarkDuplicatesMap
ReadEndsForMarkDuplicatesMap
ReadEndsForMarkDuplicatesWithBarcodes
ReadEndsForMarkDuplicatesWithBarcodesCodec
ReadEndsForMateCigar
ReadErrorCorrector
ReadErrorCorrector.CorrectionSet
ReaderSplitter
ReadFilter
ReadFilter.ReadFilterAnd
ReadFilter.ReadFilterBinOp
ReadFilterArgumentDefinitions
ReadFilteringIterator
ReadFilterLibrary
ReadFilterLibrary.AllowAllReadsReadFilter
ReadFilterLibrary.CigarContainsNoNOperator
ReadFilterLibrary.FirstOfPairReadFilter
ReadFilterLibrary.GoodCigarReadFilter
ReadFilterLibrary.HasReadGroupReadFilter
ReadFilterLibrary.MappedReadFilter
ReadFilterLibrary.MappingQualityAvailableReadFilter
ReadFilterLibrary.MappingQualityNotZeroReadFilter
ReadFilterLibrary.MatchingBasesAndQualsReadFilter
ReadFilterLibrary.MateDifferentStrandReadFilter
ReadFilterLibrary.MateOnSameContigOrNoMappedMateReadFilter
ReadFilterLibrary.NonZeroFragmentLengthReadFilter
ReadFilterLibrary.NonZeroReferenceLengthAlignmentReadFilter
ReadFilterLibrary.NotDuplicateReadFilter
ReadFilterLibrary.NotSecondaryAlignmentReadFilter
ReadFilterLibrary.NotSupplementaryAlignmentReadFilter
ReadFilterLibrary.PairedReadFilter
ReadFilterLibrary.PassesVendorQualityCheckReadFilter
ReadFilterLibrary.PrimaryLineReadFilter
ReadFilterLibrary.ProperlyPairedReadFilter
ReadFilterLibrary.ReadLengthEqualsCigarLengthReadFilter
ReadFilterLibrary.SecondOfPairReadFilter
ReadFilterLibrary.SeqIsStoredReadFilter
ReadFilterLibrary.ValidAlignmentEndReadFilter
ReadFilterLibrary.ValidAlignmentStartReadFilter
ReadFilterSparkifier
ReadGroupBlackListReadFilter
ReadGroupCovariate
ReadGroupIdSplitter
ReadGroupReadFilter
ReadGroupSplitter
ReadInputArgumentCollection
ReadLengthReadFilter
ReadLikelihoodCalculationEngine
ReadLikelihoodCalculationEngine.Implementation
ReadLikelihoods
ReadMetadata
ReadMetadata.LibraryRawStatistics
ReadMetadata.LibraryRawStatistics.Serializer
ReadMetadata.PartitionBounds
ReadMetadata.PartitionBounds.Serializer
ReadMetadata.PartitionStatistics
ReadMetadata.PartitionStatistics.Serializer
ReadMetadata.Serializer
ReadNameEncoder
ReadNameParser
ReadNameReadFilter
ReadPileup
ReadPosition
ReadPosRankSumTest
ReadQueryNameComparator
ReadRecalibrationInfo
ReadsContext
ReadsDataSource
ReadsDownsampler
ReadsDownsamplingIterator
ReadsForQNamesFinder
ReadsIterable
ReadsKey
ReadsPipelineSpark
ReadsPreprocessingPipelineTestData
ReadsSparkSink
ReadsSparkSink.SparkBAMOutputFormat
ReadsSparkSink.SparkCRAMOutputFormat
ReadsSparkSink.SparkHeaderlessBAMOutputFormat
ReadsSparkSink.SparkHeaderlessCRAMOutputFormat
ReadsSparkSink.SparkHeaderlessSAMOutputFormat
ReadsSparkSink.SparkSAMOutputFormat
ReadsSparkSource
ReadStrandFilter
ReadStructure
ReadsWriteFormat
ReadThreadingAssembler
ReadThreadingAssemblerArgumentCollection
ReadThreadingGraph
ReadTransformer
ReadTransformerSparkifier
ReadTransformingIterator
ReadType
ReadUtils
ReadUtils.ClippingTail
ReadWalker
ReadWalkerContext
ReadWalkerSpark
RealignmentArgumentCollection
RealignmentEngine
RealignmentEngine.RealignmentResult
RecalDatum
RecalibrationArgumentCollection
RecalibrationReport
RecalibrationTables
RecalUtils
ReducibleAnnotation
ReducibleAnnotationData
ReferenceArgumentCollection
ReferenceBases
ReferenceBases
ReferenceConfidenceMode
ReferenceConfidenceModel
ReferenceConfidenceVariantContextMerger
ReferenceConfidenceVariantContextMerger.VCWithNewAlleles
ReferenceContext
ReferenceDataSource
ReferenceDiploidExactAFCalculator
ReferenceFileSource
ReferenceFileSource
ReferenceHadoopSource
ReferenceInputArgumentCollection
ReferenceMemorySource
ReferenceMultiSource
ReferenceProgramGroup
ReferenceShard
ReferenceSource
ReferenceTwoBitSource
ReferenceUtils
ReferenceWindowFunctions
ReferenceWindowFunctions.FixedWindowFunction
RefFlatReader
RefFlatReader.RefFlatColumns
ReflectionUtil
RemoveNearbyIndels
RenameSampleInVcf
ReorderSam
ReorderSam.ReorderSamReferenceArgumentCollection
ReplaceSamHeader
RepresentativeReadIndexer
RepresentativeReadIndexerCodec
RequiredFeatureInputArgumentCollection
RequiredIntervalArgumentCollection
RequiredReadInputArgumentCollection
RequiredReferenceArgumentCollection
RequiredReferenceInputArgumentCollection
RequiredVariantInputArgumentCollection
ReservoirDownsampler
Resource
RevertBaseQualityScores
RevertOriginalBaseQualitiesAndAddMateCigar
RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
RevertSam
RevertSam.FileType
RExecutor
RMSMappingQuality
RnaSeqMetrics
RnaSeqMetricsCollector
RnaSeqMetricsCollector.StrandSpecificity
RobustBrentSolver
RrbsCpgDetailMetrics
RrbsMetricsCollector
RrbsSummaryMetrics
RScriptExecutor
RScriptExecutorException
RScriptLibrary
RuntimeUtils
SamAlignmentMerger
SamAlignmentMerger
SamAssertionUtils
SamComparison
SAMFileDestination
SAMFileGATKReadWriter
SamFileTester
SamFormatConverter
SAMPileupCodec
SAMPileupElement
SAMPileupFeature
Sample
SampleDB
SampleDBBuilder
SampleList
SampleList
SampleLocatableMetadata
SampleMetadata
SampleNameSplitter
SampleReadFilter
SamReaderQueryingIterator
SAMRecordAndReference
SAMRecordAndReference
SAMRecordAndReferenceMultiLevelCollector
SAMRecordAndReferenceMultiLevelCollector
SAMRecordMultiLevelCollector
SAMRecordMultiLevelCollector
SAMRecordSerializer
SAMRecordSparkCodec
SAMRecordToGATKReadAdapter
SAMRecordToGATKReadAdapterSerializer
SAMRecordToReadIterator
SamRecordWithOrdinalAndSetDuplicateReadFlag
SamRecordWithOrdinalAndSetDuplicateReadFlag
SamToFastq
SamToFastqWithTags
SATagBuilder
ScatterIntervalsByNs
ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection
ScriptExecutor
ScriptExecutorException
SeekableByteChannelPrefetcher
SegmentedCpxVariantSimpleVariantExtractor
SegmentedCpxVariantSimpleVariantExtractor.ExtractedSimpleVariants
SelectVariants
SeqGraph
SequenceComparison
SequenceDictionaryUtils
SequenceDictionaryUtils.SequenceDictionaryCompatibility
SequenceDictionaryValidationArgumentCollection
SequenceDictionaryValidationArgumentCollection.NoValidationCollection
SequenceDictionaryValidationArgumentCollection.StandardValidationCollection
SequencerFlowClass
SequencingArtifactMetrics
SequencingArtifactMetrics.BaitBiasDetailMetrics
SequencingArtifactMetrics.BaitBiasSummaryMetrics
SequencingArtifactMetrics.PreAdapterDetailMetrics
SequencingArtifactMetrics.PreAdapterSummaryMetrics
SeqVertex
SerializableFunction
SerializableOpticalDuplicatesFinder
SetNmAndUqTags
SetNmMdAndUqTags
SetSizeUtils
Sex
Sex
Shard
ShardBoundary
ShardBoundaryShard
ShardedIntervalIterator
ShardToMultiIntervalShardAdapter
SharedSequenceMerger
SharedVertexSequenceSplitter
ShortVariantDiscoveryProgramGroup
ShuffleJoinReadsWithRefBases
ShuffleJoinReadsWithVariants
SimpleAnnotatedIntervalWriter
SimpleChimera
SimpleChimera.Serializer
SimpleCopyRatioCaller
SimpleCount
SimpleCountCollection
SimpleGermlineTagger
SimpleInterval
SimpleIntervalCollection
SimpleKeyXsvFuncotationFactory
SimpleKeyXsvFuncotationFactory.XsvDataKeyType
SimpleLocatableMetadata
SimpleMarkDuplicatesWithMateCigar
SimpleNovelAdjacencyAndChimericAlignmentEvidence
SimpleNovelAdjacencyAndChimericAlignmentEvidence.Serializer
SimpleNovelAdjacencyInterpreter
SimpleRepeatMaskTransformer
SimpleSampleLocatableMetadata
SimpleSampleMetadata
SimpleSVD
SimpleSVType
SimpleSVType.Deletion
SimpleSVType.DuplicationInverted
SimpleSVType.DuplicationTandem
SimpleSVType.ImpreciseDeletion
SimpleSVType.Insertion
SimpleSVType.Inversion
SimpleSVType.TYPES
SinglePassSamProgram
SingleSequenceReferenceAligner
SingleSequenceReferenceAligner.TriFunction
SingularValueDecomposer
SliceSampler
SmithWatermanAligner
SmithWatermanAligner.Implementation
SmithWatermanAlignment
SmithWatermanIntelAligner
SmithWatermanJavaAligner
SmithWatermanJavaAligner.State
Snp
SomaticGenotypingEngine
SomaticLikelihoodsEngine
SortSam
SortSamSpark
SortVcf
SparkCommandLineArgumentCollection
SparkCommandLineProgram
SparkContextFactory
SparkConverter
SparkSharder
SparkSingularValueDecomposer
SparkTestUtils
SparkUtils
SplitIntervals
SplitNCigarReads
SplitReads
SplitSamByLibrary
SplitSamByNumberOfReads
SplitVcfs
StandardAnnotation
StandardArgumentDefinitions
StandardCallerArgumentCollection
StandardCovariateList
StandardHCAnnotation
StandardMutectAnnotation
StandardOptionDefinitions
Strand
Strand.Serializer
StrandArtifact
StrandArtifact.ArtifactState
StrandBiasBySample
StrandBiasTest
StrandedInterval
StrandedInterval.Serializer
StrandOddsRatio
StrandSwitch
StreamingProcessController
StreamingPythonScriptExecutor
StreamLocation
StreamOutput
StripMateNumberTransformer
StructuralVariantDiscoveryProgramGroup
StructuralVariationDiscoveryArgumentCollection
StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigsAlignmentsSparkArgumentCollection
StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
StructuralVariationDiscoveryPipelineSpark
StructuralVariationDiscoveryPipelineSpark.InMemoryAlignmentParser
SubsettedLikelihoodMatrix
SvCigarUtils
SVContext
SVD
SVDDenoisedCopyRatioResult
SVDDenoisingUtils
SVDFactory
SvDiscoverFromLocalAssemblyContigAlignmentsSpark
SvDiscoverFromLocalAssemblyContigAlignmentsSpark.AssemblyContigsClassifiedByAlignmentSignatures
SvDiscoverFromLocalAssemblyContigAlignmentsSpark.SAMFormattedContigAlignmentParser
SvDiscoveryInputMetaData
SvDiscoveryInputMetaData.ReferenceData
SvDiscoveryInputMetaData.SampleSpecificData
SvDiscoveryUtils
SVDReadCountPanelOfNormals
SVDUSTFilteredKmerizer
SVFastqUtils
SVFastqUtils.FastqRead
SVFastqUtils.FastqRead.Serializer
SVFastqUtils.Mapping
SVFileUtils
SVInterval
SVInterval.Serializer
SVIntervalTree
SVIntervalTree.Entry
SVIntervalTree.Serializer
SVIntervalTree.ValuesIterator
SVKmer
SVKmer.Base
SVKmerizer
SVKmerizer.ASCIICharSequence
SVKmerLong
SVKmerLong.Serializer
SVKmerShort
SVKmerShort.Serializer
SVLocation
SVReadFilter
SVReferenceUtils
SvType
SVUtils
SVUtils.IteratorFilter
SVVCFReader
SVVCFWriter
SWNativeAlignerWrapper
SynchronizedUnivariateSolver
SynchronizedUnivariateSolver.UnivariateSolverStatus
SystemProperty
TabbedInputParser
TabbedTextFileWithHeaderParser
TableCodec
TableColumnCollection
TableFeature
TableFuncotation
TableReader
TableUtils
TableWriter
TagGermlineEvents
TandemRepeat
TargetedPcrMetrics
TargetedPcrMetricsCollector
TargetMetrics
TargetMetricsCollector
TargetMetricsCollector.Coverage
TemplateFragmentOrdinal
TensorType
Test
Testing
TestingReadThreadingGraph
TestProgramGroup
TextFormattingUtils
TextMDCodec
TextMDCodec.DeletionMDElement
TextMDCodec.MatchMDElement
TextMDCodec.MDElement
TextMDCodec.MismatchMDElement
TheoreticalSensitivity
TheoreticalSensitivity.RouletteWheel
ThreadPoolExecutorWithExceptions
Tile
TileIndex
TileIndex.TileIndexRecord
TileMetricsOutReader
TileMetricsOutReader.IlluminaLaneTileCode
TileMetricsOutReader.IlluminaTileMetrics
TileMetricsOutReader.TileMetricsVersion
TileMetricsUtil
TilePhasingValue
TileTemplateRead
TrainingSet
Tranche
Tranche.TrancheComparator
Tranche.TrancheTruthSensitivityComparator
TrancheManager
TrancheManager.SelectionMetric
TrancheManager.TruthSensitivityMetric
TranscriptSelectionMode
Transition
Transition
Transition.Base
TraversalParameters
Trilean
Trio
TwoPassReadWalker
TwoPassVariantWalker
UmiAwareMarkDuplicatesWithMateCigar
UmiGraph
UmiMetrics
UmiUtil
UnfilledReadsLikelihoods
UnifiedArgumentCollection
UniqueAltReadCount
UniqueIDWrapper
UnivariateSolverJobDescription
UnivariateSolverSpecifications
UnmarkDuplicates
UnsignedTypeUtil
UnsignedTypeUtil
UpdateVCFSequenceDictionary
UpdateVcfSequenceDictionary
UserException
UserException.BadInput
UserException.BadTempDir
UserException.CannotExecuteScript
UserException.CannotHandleGzippedRef
UserException.CouldNotCreateOutputFile
UserException.CouldNotIndexFile
UserException.CouldNotReadInputFile
UserException.EmptyIntersection
UserException.FailsStrictValidation
UserException.HardwareFeatureException
UserException.HeaderMissingReadGroup
UserException.IncompatibleRecalibrationTableParameters
UserException.IncompatibleSequenceDictionaries
UserException.LexicographicallySortedSequenceDictionary
UserException.MalformedBAM
UserException.MalformedFile
UserException.MalformedGenomeLoc
UserException.MalformedRead
UserException.MisencodedQualityScoresRead
UserException.MissingContigInSequenceDictionary
UserException.MissingIndex
UserException.MissingReference
UserException.MissingReferenceDictFile
UserException.MissingReferenceFaiFile
UserException.NoSuitableCodecs
UserException.ReadMissingReadGroup
UserException.Require2BitReferenceForBroadcast
UserException.UnimplementedFeature
UserException.WrongFeatureType
Utils
ValidateBasicSomaticShortMutations
ValidateSamFile
ValidateSamFile.Mode
ValidateVariants
ValidateVariants.ValidationType
VariantAccumulatorExecutor
VariantAccumulatorExecutor.MultiThreadedChunkBased
VariantAnnotation
VariantAnnotator
VariantAnnotatorEngine
VariantAnnotatorEngine.VAExpression
VariantCallContext
VariantContextTestUtils
VariantContextVariantAdapter
VariantDataManager
VariantEvaluationProgramGroup
VariantFilter
VariantFilter
VariantFilteringProgramGroup
VariantFilterLibrary
VariantFiltration
VariantIDsVariantFilter
VariantIteratorProducer
VariantManipulationProgramGroup
VariantOverlapAnnotator
VariantProcessor
VariantProcessor.Accumulator
VariantProcessor.AccumulatorGenerator
VariantProcessor.Builder
VariantProcessor.ResultMerger
VariantRecalibrator
VariantRecalibratorEngine
VariantShard
VariantsSource
VariantsSparkSink
VariantsSparkSink.GvcfKeyIgnoringVCFRecordWriter
VariantsSparkSink.SparkHeaderlessVCFOutputFormat
VariantsSparkSink.SparkVCFOutputFormat
VariantsSparkSource
VariantsToTable
VariantType
VariantTypesVariantFilter
VariantUtils
VariantWalker
VariantWalkerBase
VariantWalkerContext
VariantWalkerSpark
VcfFileSegment
VcfFileSegmentGenerator
VcfFormatConverter
VcfFuncotationFactory
VcfOutputRenderer
VcfToIntervalList
VcfUtils
VcfUtils
VectorLoglessPairHMM
VectorLoglessPairHMM.Implementation
ViewSam
ViewSam.AlignmentStatus
ViewSam.PfStatus
ViterbiAlgorithm
VQSLODTranche
WellformedReadFilter
WgsMetricsProcessor
WgsMetricsProcessorImpl
XorWrapper
XReadLines
XsvLocatableTableCodec
XsvTableFeature