All Classes
AbstractAlignmentMerger
AbstractAlignmentMerger
AbstractAlignmentMerger.UnmappingReadStrategy
AbstractConcordanceWalker
AbstractConcordanceWalker.TruthVersusEval
AbstractIlluminaPositionFileReader
AbstractInputParser
AbstractLocatableCollection
AbstractMarkDuplicatesCommandLineProgram
AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
AbstractOpticalDuplicateFinderCommandLineProgram
AbstractRecordCollection
AbstractSampleLocatableCollection
AbstractSampleRecordCollection
AbstractWgsMetricsCollector
AccumulateVariantCallingMetrics
ActivityProfile
ActivityProfileState
ActivityProfileState.Type
ActivityProfileStateIterator
ActivityProfileStateRange
AdapterMarker
AdapterPair
AdapterPair
AdapterTrimTransformer
AdapterUtility
AdaptiveChainPruner
AdaptiveMetropolisSampler
AddCommentsToBam
AddOATag
AddOriginalAlignmentTags
AddOrReplaceReadGroups
AFCalculationResult
Affection
AFPriorProvider
AliasProvider
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
AlleleCount
AlleleFraction
AlleleFractionCluster
AlleleFractionKernelSegmenter
AlleleFractionModeller
AlleleFractionParameter
AlleleFractionPrior
AlleleFractionSegment
AlleleFractionSegmentCollection
AlleleFrequency
AlleleFrequency.StratifyingScale
AlleleFrequencyCalculator
AlleleFrequencyExacUtils
AlleleFrequencyQC
AlleleFrequencyQCMetric
AlleleFrequencyUtils
AlleleLikelihoodMatrixMapper
AlleleLikelihoods
AlleleList
AlleleList.ActualPermutation
AlleleList.NonPermutation
AlleleListPermutation
AllelePileupCounter
AlleleSpecificAnnotation
AlleleSpecificAnnotationData
AlleleSubsettingUtils
AlleleSubsettingUtils
AllelicCount
AllelicCountCollection
AllelicCountCollector
AllLocusIterator
AltSiteRecord
AltSiteRecord.AltSiteRecordTableWriter
AmbiguousBaseReadFilter
AminoAcid
Analysis
AnalysisModuleScanner
AnalyzeCovariates
AnalyzeSaturationMutagenesis
AnalyzeSaturationMutagenesis.ReportTypeCounts
AnnotatedInterval
AnnotatedInterval
AnnotatedIntervalCodec
AnnotatedIntervalCollection
AnnotatedIntervalCollection
AnnotatedIntervalHeader
AnnotatedIntervalToSegmentVariantContextConverter
AnnotatedIntervalUtils
AnnotatedIntervalWriter
AnnotatedVariantProducer
AnnotateIntervals
AnnotatePairOrientation
AnnotateVcfWithBamDepth
AnnotateVcfWithExpectedAlleleFraction
Annotation
AnnotationException
AnnotationKey
AnnotationMap
AnnotationUtils
ApacheSingularValueDecomposer
ApplyBQSR
ApplyBQSRArgumentCollection
ApplyBQSRSpark
ApplyBQSRSparkFn
ApplyBQSRUniqueArgumentCollection
ApplyVQSR
ArHetvarFilter
ArHomvarFilter
ArraysControlInfo
ArtifactPrior
ArtifactPrior.ArtifactPriorTableReader
ArtifactPrior.ArtifactPriorTableWriter
ArtifactPriorCollection
ArtifactState
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
AssemblyBasedCallerUtils
AssemblyContigAlignmentsConfigPicker
AssemblyContigAlignmentsConfigPicker.GoodAndBadMappings
AssemblyContigWithFineTunedAlignments
AssemblyContigWithFineTunedAlignments.AlignmentSignatureBasicType
AssemblyContigWithFineTunedAlignments.ReasonForAlignmentClassificationFailure
AssemblyContigWithFineTunedAlignments.Serializer
AssemblyRegion
AssemblyRegionArgumentCollection
AssemblyRegionEvaluator
AssemblyRegionFromActivityProfileStateIterator
AssemblyRegionIterator
AssemblyRegionReadShardArgumentCollection
AssemblyRegionTrimmer
AssemblyRegionTrimmer.Result
AssemblyRegionWalker
AssemblyRegionWalkerContext
AssemblyRegionWalkerSpark
AssemblyResult
AssemblyResult.Status
AssemblyResultSet
AsynchronousStreamWriter
AsyncIterator
AtomicIterator
AutoCloseableCollection
AutosomalRecessiveConstants
BaitDesigner
BaitDesigner.DesignStrategy
BamIndexStats
BamToBfq
BamToBfqWriter
BandPassActivityProfile
BAQ
BAQ.BAQCalculationResult
BAQ.CalculationMode
BAQ.QualityMode
BarcodeEditDistanceQuery
BarcodeFileFaker
BarcodeFileReader
BaseBclReader
BaseCalculator
BaseCallingProgramGroup
BaseDistributionByCycleMetrics
BaseDistributionByCycleMetrics
BaseEdge
BaseErrorAggregation
BaseErrorCalculator
BaseErrorMetric
BaseGraph
BaseIlluminaDataProvider
BaselineCopyNumberCollection
BaseQuality
BaseQualityClipReadTransformer
BaseQualityFilter
BaseQualityHistogram
BaseQualityRankSumTest
BaseQualityReadTransformer
BaseRecalibrationEngine
BaseRecalibrationEngine.BQSRReferenceWindowFunction
BaseRecalibrator
BaseRecalibratorSpark
BaseRecalibratorSparkFn
BaseUtils
BaseUtils.Base
BaseUtils.BaseSubstitutionType
BaseVertex
BasicInputParser
BasicSomaticShortMutationValidator
BasicValidationResult
BciFileFaker
BclData
BclFileFaker
BclIndexReader
BclQualityEvaluationStrategy
BclReader
BDGAlignmentRecordToGATKReadAdapter
BedToIntervalList
BestEndMapqPrimaryAlignmentStrategy
BestEndMapqPrimaryAlignmentStrategy
BestMapqPrimaryAlignmentSelectionStrategy
BestMapqPrimaryAlignmentSelectionStrategy
BetaBinomialCluster
BetaBinomialDistribution
BetaDistributionShape
BinomialCluster
BQSRPipelineSpark
BQSRReadTransformer
BreakEndVariantType
BreakEndVariantType.InterChromosomeBreakend
BreakEndVariantType.IntraChromosomalStrandSwitch33BreakEnd
BreakEndVariantType.IntraChromosomalStrandSwitch55BreakEnd
BreakEndVariantType.IntraChromosomeRefOrderSwap
BreakEndVariantType.SupportedType
BreakpointComplications
BreakpointComplications.IntraChrStrandSwitchBreakpointComplications
BreakpointComplications.IntraChrStrandSwitchBreakpointComplications.Serializer
BreakpointComplications.InvertedDuplicationBreakpointComplications
BreakpointComplications.InvertedDuplicationBreakpointComplications.Serializer
BreakpointComplications.SimpleInsDelOrReplacementBreakpointComplications
BreakpointComplications.SimpleInsDelOrReplacementBreakpointComplications.Serializer
BreakpointComplications.SmallDuplicationBreakpointComplications
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
BreakpointsInference
BucketUtils
Build37ExtendedIlluminaManifest
Build37ExtendedIlluminaManifestRecord
Build37ExtendedIlluminaManifestRecord.Flag
BuildBamIndex
BunnyLog
BwaAndMarkDuplicatesPipelineSpark
BwaArgumentCollection
BwaMemAlignmentUtils
BwaMemIndexCache
BwaMemIndexImageCreator
BwaSpark
BwaSparkEngine
ByIntervalListVariantContextIterator
ByteArrayIterator
CachingIndexedFastaSequenceFile
CalcMetadataSpark
CalculateContamination
CalculateFingerprintMetrics
CalculateGenotypePosteriors
CalculateMixingFractions
CalculateReadGroupChecksum
CallCopyRatioSegments
CalledCopyRatioSegment
CalledCopyRatioSegment.Call
CalledCopyRatioSegmentCollection
CalledHaplotypes
CalledLegacySegment
CalledLegacySegmentCollection
CallingMetricAccumulator
CallingMetricAccumulator.Result
CapturedStreamOutput
CapturedStreamOutputSnapshot
Casava18ReadNameEncoder
CbclData
CbclReader
ChainPruner
ChannelAsSeekableStream
CheckFingerprint
CheckIlluminaDirectory
CheckPileup
CheckTerminatorBlock
ChimeraUtil
ChimericOriginalAlignmentFilter
ChromosomeCounts
CigarUtils
CircularByteBuffer
ClassFinder
ClassUtils
CleanSam
ClinVarFilter
ClippingOp
ClippingRankSumTest
ClippingRepresentation
ClippingUtility
ClipReads
ClipReads.ClippingData
ClipReads.ReadClipperWithData
ClocsFileFaker
ClocsFileReader
CloseAtEndIterator
ClusterCrosscheckMetrics
ClusterData
ClusterDataToSamConverter
ClusteredCrosscheckMetric
ClusteredEventsFilter
CNNScoreVariants
CNNVariantTrain
CNNVariantWriteTensors
CNVInputReader
CollectAlignmentSummaryMetrics
CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection
CollectAllelicCounts
CollectAllelicCountsSpark
CollectArraysVariantCallingMetrics
CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics
CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
CollectBaseDistributionByCycle
CollectBaseDistributionByCycleSpark
CollectF1R2Counts
CollectF1R2CountsArgumentCollection
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
CollectReadCounts.Format
CollectRnaSeqMetrics
CollectRrbsMetrics
CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection
CollectSamErrorMetrics
CollectSequencingArtifactMetrics
CollectTargetedMetrics
CollectTargetedPcrMetrics
CollectVariantCallingMetrics
CollectVariantCallingMetrics.VariantCallingDetailMetrics
CollectVariantCallingMetrics.VariantCallingSummaryMetrics
CollectWgsMetrics
CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection
CollectWgsMetrics.WgsMetricsCollector
CollectWgsMetricsWithNonZeroCoverage
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
CombineGVCFs
CombineSegmentBreakpoints
CommandLineDefaults
CommandLineProgram
CommandLineProgram
CommandLineSyntaxTranslater
CommonSuffixSplitter
CompareBaseQualities
CompareDuplicatesSpark
CompareIntervalLists
CompareMatrix
CompareMetrics
CompareSAMs
CompFeatureInput
ComplexityPartitioner
CompositeOutputRenderer
CompOverlap
CompressedDataList
Concordance
ConcordanceState
ConcordanceSummaryRecord
ConcordanceSummaryRecord.Reader
ConcordanceSummaryRecord.Writer
ConfigFactory
ContainsKmerReadFilter
ContainsKmerReadFilterSpark
ContaminationFilter
ContaminationModel
ContaminationRecord
ContaminationSegmenter
ContextCovariate
Contig
ContigAlignmentsModifier
ContigAlignmentsModifier.AlnModType
ContigAlignmentsModifier.AlnModType.ModTypeString
ContigChimericAlignmentIterativeInterpreter
ConvertHeaderlessHadoopBamShardToBam
ConvertSequencingArtifactToOxoG
CopyNumberAnnotations
CopyNumberArgumentValidationUtils
CopyNumberFormatsUtils
CopyNumberPosteriorDistribution
CopyNumberPosteriorDistributionCollection
CopyNumberProgramGroup
CopyNumberStandardArgument
CopyRatio
CopyRatioCollection
CopyRatioKernelSegmenter
CopyRatioModeller
CopyRatioParameter
CopyRatioSegment
CopyRatioSegmentCollection
CosmicFuncotationFactory
CountBases
CountBasesInReference
CountBasesSpark
CounterManager
CountFalsePositives
CountingAdapterFilter
CountingDuplicateFilter
CountingFilter
CountingMapQFilter
CountingPairedFilter
CountingReadFilter
CountingReadFilter.CountingAndReadFilter
CountingVariantFilter
CountingVariantFilter.CountingAndVariantFilter
CountNs
CountReads
CountReadsSpark
CountVariants
CountVariants
CountVariantsSpark
Covariate
CovariateKeyCache
Coverage
CoverageAnalysisProgramGroup
CoveragePerContig
CoveragePerContigCollection
CpG
CpxVariantInterpreter
CpxVariantReInterpreterSpark
CreateHadoopBamSplittingIndex
CreateReadCountPanelOfNormals
CreateSequenceDictionary
CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection
CreateSomaticPanelOfNormals
CreateVerifyIDIntensityContaminationMetricsFile
CrosscheckFingerprints
CrosscheckMetric
CrosscheckMetric.DataType
CrosscheckMetric.FingerprintResult
CrosscheckReadGroupFingerprints
CsvInputParser
CustomAFPriorProvider
CustomBooleanConverter
CustomMafFuncotationCreator
CycleCovariate
DataCollection
DataLine
DataPoint
DataSourceFuncotationFactory
DataSourceUtils
Datum
DbsnpArgumentCollection
DbSnpBitSetUtil
DbSnpBitSetUtil
DbSnpBitSetUtil.DbSnpBitSets
DbSnpBitSetUtil.DbSnpBitSets
DbSnpVariantType
Decile
DecileCollection
DefaultGATKReadFilterArgumentCollection
DefaultGATKVariantAnnotationArgumentCollection
Degeneracy
DelimitedTextFileWithHeaderIterator
DenoiseReadCounts
DeprecatedToolsRegistry
DepthFilter
DepthOneHistograms
DepthPerAlleleBySample
DepthPerSampleHC
DetermineGermlineContigPloidy
DetermineGermlineContigPloidy.RunMode
DiagnosticsAndQCProgramGroup
DigammaCache
DiploidGenotype
DiploidHaplotype
Dirichlet
DiscoverVariantsFromContigAlignmentsSAMSpark
DiskBasedReadEndsForMarkDuplicatesMap
DistanceMetric
DoNotSubclass
DownsampleableSparkReadShard
Downsampler
DownsampleSam
DownsampleType
DownsamplingMethod
DuplicatedAltReadFilter
DuplicationMetrics
DUSTReadTransformer
EarliestFragmentPrimaryAlignmentSelectionStrategy
EarliestFragmentPrimaryAlignmentSelectionStrategy
EmpiricalPhasingMetricsOutReader
EmpiricalPhasingMetricsOutReader.IlluminaPhasingMetrics
EmptyFragment
ErrorMetric
ErrorProbabilities
ErrorSummaryMetrics
ErrorType
EstimateLibraryComplexity
EvalFeatureInput
EvaluateInfoFieldConcordance
EvaluationContext
EventMap
EventType
EvidenceFeatures
EvidenceOverlapChecker
EvidenceTargetLink
EvidenceTargetLink.Serializer
EvidenceTargetLinkClusterer
ExampleAssemblyRegionWalker
ExampleAssemblyRegionWalkerSpark
ExampleAssemblyRegionWalkerSpark.ExampleAssemblyRegionArgumentCollection
ExampleCollectMultiMetricsSpark
ExampleCollectSingleMetricsSpark
ExampleFeatureWalker
ExampleIntervalWalker
ExampleIntervalWalkerSpark
ExampleLocusWalker
ExampleLocusWalkerSpark
ExampleMultiMetrics
ExampleMultiMetricsArgumentCollection
ExampleMultiMetricsCollector
ExampleMultiMetricsCollectorSpark
ExampleNioCountReads
ExamplePostTraversalPythonExecutor
ExampleProgramGroup
ExampleReadWalkerWithReference
ExampleReadWalkerWithReferenceSpark
ExampleReadWalkerWithVariants
ExampleReadWalkerWithVariantsSpark
ExampleReferenceWalker
ExampleSingleMetrics
ExampleSingleMetricsArgumentCollection
ExampleSingleMetricsCollectorSpark
ExampleStreamingPythonExecutor
ExampleTwoPassVariantWalker
ExampleVariantWalker
ExampleVariantWalkerSpark
ExcessHet
ExomeStandardArgumentDefinitions
ExtractIlluminaBarcodes
ExtractIlluminaBarcodes.BarcodeMetric
ExtractIlluminaBarcodes.PerTileBarcodeExtractor
ExtractIlluminaBarcodes.PerTileBarcodeExtractor.BarcodeMatch
ExtractOriginalAlignmentRecordsByNameSpark
ExtractSequences
ExtractSVEvidenceSpark
F1R2CountsCollector
F1R2FilterConstants
F1R2FilterUtils
FalsePositiveRecord
Family
FamilyLikelihoods
FastaAlternateReferenceMaker
FastaReferenceMaker
FastqToSam
FastWgsMetricsCollector
FeatureContext
FeatureDataSource
FeatureInput
FeatureManager
FeatureWalker
FermiLiteAssemblyHandler
FifoBuffer
FileFaker
Filter
FilterAlignmentArtifacts
FilterAnalysisRecord
FilterApplyingVariantIterator
FilterByOrientationBias
FilteredHaplotypeFilter
FilterFileFaker
FilterFileReader
FilterFuncotations
FilterFuncotations.AlleleFrequencyDataSource
FilterFuncotations.Reference
FilterFuncotationsConstants
FilterFuncotationsUtils
FilteringOutputStats
FilterIntervals
FilterMutectCalls
FilterSamReads
FilterSamReads.Filter
FilterStats
FilterType
FilterVariantTranches
FilterVcf
FindAssemblyRegionsSpark
FindBadGenomicKmersSpark
FindBreakpointEvidenceSpark
FindBreakpointEvidenceSpark.AssembledEvidenceResults
FindBreakpointEvidenceSpark.IntPair
FindMendelianViolations
Fingerprint
FingerprintChecker
FingerprintIdDetails
FingerprintingDetailMetrics
FingerprintingSummaryMetrics
FingerprintMetrics
FingerprintResults
FingerprintUtils
FingerprintUtils.VariantContextSet
FisherExactTest
FisherStrand
FisherStrandFilter
FixCallSetSampleOrdering
FixMateInformation
FixMisencodedBaseQualityReads
FixVcfHeader
FlagStat
FlagStat.FlagStatus
FlagStatSpark
FlankSettings
FlatMapGluer
ForwardBackwardAlgorithm
ForwardBackwardAlgorithm.Result
FourChannelIntensityData
FractionalDownsampler
Fragment
Fragment
FragmentCollection
FragmentLength
FragmentLengthFilter
FragmentLengthReadFilter
FragmentUtils
FuncotateSegments
Funcotation
FuncotationFilter
FuncotationMap
FuncotationMetadata
FuncotationMetadataUtils
Funcotator
FuncotatorArgumentDefinitions
FuncotatorArgumentDefinitions.DataSourceType
FuncotatorArgumentDefinitions.OutputFormatType
FuncotatorConstants
FuncotatorDataSourceDownloader
FuncotatorEngine
FuncotatorSegmentArgumentCollection
FuncotatorUtils
FuncotatorUtils.Genus
FuncotatorUtils.TranscriptCodingSequenceException
FuncotatorVariantArgumentCollection
FunctionalClass
FunctionalClass.FunctionalType
GA4GHScheme
GA4GHSchemeWithMissingAsHomRef
GatherBamFiles
GatherBQSRReports
GatherPileupSummaries
GatherTranches
GatherVcfs
GatherVcfsCloud
GatherVcfsCloud.GatherType
GATKAnnotationArgumentCollection
GATKAnnotationPluginDescriptor
GATKConfig
GATKDataSource
GATKDocWorkUnit
GATKDuplicationMetrics
GATKException
GATKException.MissingReadField
GATKException.ReadAttributeTypeMismatch
GATKException.ShouldNeverReachHereException
GATKGSONWorkUnit
GATKHelpDoclet
GATKHelpDocWorkUnitHandler
GATKPathSpecifier
GATKProtectedVariantContextUtils
GATKRead
GATKReadFilterArgumentCollection
GATKReadFilterPluginDescriptor
GATKReadToBDGAlignmentRecordConverter
GATKReadWriter
GATKRegistrator
GATKReport
GATKReportColumn
GATKReportColumnFormat
GATKReportColumnFormat.Alignment
GATKReportDataType
GATKReportTable
GATKReportTable.Sorting
GATKReportTable.TableDataHeaderFields
GATKReportTable.TableNameHeaderFields
GATKReportVersion
GATKSparkTool
GATKSparkTool.ReadInputMergingPolicy
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
GeneListOutputRenderer
GenomeLoc
GenomeLocParser
GenomeLocParser.ValidationLevel
GenomeLocSortedSet
GenomicsDBBCFCodec
GenomicsDBConstants
GenomicsDBImport
GenomicsDBOptions
GenomicsDBUtils
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
GenotypeFilterSummary
GenotypeGVCFs
GenotypeGVCFsEngine
GenotypeLikelihoodCalculator
GenotypeLikelihoodCalculators
GenotypeLikelihoodsCalculationModel
GenotypeQualityFilter
GenotypeSummaries
GenotypeUtils
GenotypingArraysProgramGroup
GenotypingData
GenotypingEngine
GenotypingLikelihoods
GermlineCallingArgumentCollection
GermlineCNVCaller
GermlineCNVCaller.RunMode
GermlineCNVHybridADVIArgumentCollection
GermlineCNVIntervalVariantComposer
GermlineCNVNamingConstants
GermlineCNVSegmentVariantComposer
GermlineCNVVariantComposer
GermlineContigPloidyHybridADVIArgumentCollection
GermlineContigPloidyModelArgumentCollection
GermlineDenoisingModelArgumentCollection
GermlineDenoisingModelArgumentCollection.CopyNumberPosteriorExpectationMode
GermlineFilter
GetPileupSummaries
GetSampleName
GibbsSampler
GnarlyGenotyper
GnarlyGenotyperEngine
GraphUtils
GraphUtils
GraphUtils.Graph
GtcToVcf
GVCFBlock
GVCFBlockCombiner
GVCFBlockCombiningIterator
GvcfMetricAccumulator
GVCFWriter
Haplotype
HaplotypeBAMDestination
HaplotypeBAMWriter
HaplotypeBAMWriter.WriterType
HaplotypeBlock
HaplotypeCaller
HaplotypeCallerArgumentCollection
HaplotypeCallerEngine
HaplotypeCallerGenotypingEngine
HaplotypeCallerReadThreadingAssemblerArgumentCollection
HaplotypeCallerSpark
HaplotypeCallerSpark.HaplotypeCallerAssemblyRegionArgumentCollection
HaplotypeMap
HaplotypeProbabilities
HaplotypeProbabilities.Genotype
HaplotypeProbabilitiesFromContaminatorSequence
HaplotypeProbabilitiesFromGenotype
HaplotypeProbabilitiesFromGenotypeLikelihoods
HaplotypeProbabilitiesFromSequence
HaplotypeProbabilityOfNormalGivenTumor
HardFilter
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
IlluminaAdpcFileWriter
IlluminaAdpcFileWriter.Record
IlluminaBasecallingMetrics
IlluminaBasecallsConverter
IlluminaBasecallsToFastq
IlluminaBasecallsToFastq.ReadNameFormat
IlluminaBasecallsToSam
IlluminaDataProvider
IlluminaDataProviderFactory
IlluminaDataType
IlluminaFileUtil
IlluminaFileUtil.SupportedIlluminaFormat
IlluminaGenotype
IlluminaLaneMetrics
IlluminaManifest
IlluminaManifestRecord
IlluminaManifestRecord.IlluminaStrand
IlluminaMetricsCode
IlluminaPhasingMetrics
IlluminaReadNameEncoder
IlluminaUtil
IlluminaUtil.IlluminaAdapterPair
ImpreciseVariantDetector
InbreedingCoeff
IndelErrorCalculator
IndelErrorMetric
IndelLengthHistogram
IndelSize
IndelSummary
IndependentReplicateMetric
IndependentSampleGenotypesModel
IndexedAlleleList
IndexedSampleList
IndexedSet
IndexFeatureFile
IndexRange
IndexUtils
InfiniumDataFile
InfiniumEGTFile
InfiniumFileTOC
InfiniumGTCFile
InfiniumGTCRecord
InfiniumNormalizationManifest
InfiniumTransformation
InfiniumVcfFields
InfiniumVcfFields.GENOTYPE_VALUES
InfoConcordanceRecord
InfoConcordanceRecord.InfoConcordanceReader
InfoConcordanceRecord.InfoConcordanceWriter
InfoFieldAnnotation
InputStreamSettings
InsertSizeDistribution
InsertSizeDistributionShape
InsertSizeMetrics
InsertSizeMetrics
InsertSizeMetricsArgumentCollection
InsertSizeMetricsCollector
InsertSizeMetricsCollector
InsertSizeMetricsCollectorSpark
IntBiConsumer
IntegerCopyNumberSegment
IntegerCopyNumberSegmentCollection
IntegerCopyNumberState
IntegrationUtils
IntensityChannel
IntervalAlignmentContextIterator
IntervalArgumentCollection
IntervalArgumentCollection
IntervalCopyNumberGenotypingData
IntervalCoverageFinder
IntervalListScatter
IntervalListScatterer
IntervalListScattererByBaseCount
IntervalListScattererByIntervalCount
IntervalListScattererWithoutSubdivision
IntervalListScattererWithoutSubdivisionWithOverflow
IntervalListScattererWithSubdivision
IntervalListScatterMode
IntervalListToBed
IntervalListTools
IntervalListTools.Action
IntervalLocusIterator
IntervalMergingRule
IntervalOverlappingIterator
IntervalOverlapReadFilter
IntervalSetRule
IntervalsManipulationProgramGroup
IntervalStratification
IntervalUtils
IntervalUtils.IntervalBreakpointType
IntervalWalker
IntervalWalkerContext
IntervalWalkerSpark
IntHistogram
IntHistogram.CDF
IntHistogram.CDF.Serializer
IntHistogram.Serializer
IntToDoubleBiFunction
IntToDoubleFunctionCache
IOUtils
Iterators
JexlExpression
JoinReadsWithVariants
JsonSerializer
JumpingLibraryMetrics
KBestHaplotype
KBestHaplotypeFinder
KernelSegmenter
KernelSegmenter.ChangepointSortOrder
Kmer
KmerAndCount
KmerAndCount.Serializer
KmerAndInterval
KmerAndInterval.Serializer
KmerCleaner
KmerCounter
KMerCounter
KmerSearchableGraph
KSWindowFinder
KV
LanePhasingMetricsCollector
LargeLongHopscotchSet
LargeLongHopscotchSet.Serializer
LearnReadOrientationModel
LearnReadOrientationModelEngine
LeftAlignAndTrimVariants
LeftAlignIndels
LegacySegment
LegacySegmentCollection
LevelingDownsampler
LibraryIdGenerator
LibraryIdGenerator
LibraryNameSplitter
LibraryReadFilter
LibraryStatistics
LibraryStatistics.Serializer
LIBSDownsamplingInfo
LiftOverIntervalList
LiftoverUtils
LiftoverVcf
LikelihoodEngineArgumentCollection
LikelihoodMatrix
LikelihoodRankSumTest
LinearCopyRatio
LinearCopyRatioCollection
LineIteratorReader
LmmFilter
LocatableFuncotationCreator
LocatableMetadata
LocatableXsvFuncotationFactory
LocsFileFaker
LocsFileReader
LocusFunction
LocusIteratorByState
LocusWalker
LocusWalkerContext
LocusWalkerSpark
LofFilter
Log10Cache
Log10FactorialCache
Log10PairHMM
LoggingUtils
LoglessPairHMM
LongBloomFilter
LongBloomFilter.Serializer
LongHopscotchSet
LongHopscotchSet.Serializer
LongIterator
LowWeightChainPruner
LRUCache
M2ArgumentCollection
M2FiltersArgumentCollection
MafOutputRenderer
MafOutputRendererConstants
Main
MakeSitesOnlyVcf
MakeVcfSampleNameMap
MannWhitneyU
MannWhitneyU.RankedData
MannWhitneyU.Result
MannWhitneyU.TestStatistic
MannWhitneyU.TestType
MappingQuality
MappingQualityFilter
MappingQualityRankSumTest
MappingQualityReadFilter
MappingQualityReadTransformer
MappingQualityZero
MarkDuplicates
MarkDuplicates.DuplicateTaggingPolicy
MarkDuplicates.DuplicateType
MarkDuplicatesScoringStrategy
MarkDuplicatesSpark
MarkDuplicatesSparkArgumentCollection
MarkDuplicatesSparkRecord
MarkDuplicatesSparkRecord.Type
MarkDuplicatesSparkUtils
MarkDuplicatesSparkUtils.IndexPair
MarkDuplicatesSparkUtils.TransientFieldPhysicalLocationComparator
MarkDuplicatesWithMateCigar
MarkDuplicatesWithMateCigarIterator
MarkedOpticalDuplicateReadFilter
MarkIlluminaAdapters
MarkQueue
MatchResults
MathUtil
MathUtil.LogMath
MathUtils
MathUtils.IntToDoubleArrayFunction
MathUtils.RunningAverage
MatrixSummaryUtils
MeanQualityByCycle
MeanQualityByCycleSpark
MendelianViolation
MendelianViolationEvaluator
MendelianViolationMetrics
MendelianViolationsByFamily
MergeableMetricBase
MergeableMetricBase.MergeByAdding
MergeableMetricBase.MergeByAssertEquals
MergeableMetricBase.MergingIsManual
MergeableMetricBase.NoMergingIsDerived
MergeableMetricBase.NoMergingKeepsValue
MergeAnnotatedRegions
MergeAnnotatedRegionsByAnnotation
MergeBamAlignment
MergeMutect2CallsWithMC3
MergeMutectStats
MergePedIntoVcf
MergeSamFiles
MergeVcfs
Metadata
Metadata.Type
MetadataUtils
MetagenomicsProgramGroup
MethylationProgramGroup
MethylationTypeCaller
MetricAccumulationLevel
MetricAccumulationLevel
MetricAccumulationLevelArgumentCollection
MetricsArgumentCollection
MetricsCollection
MetricsCollectorSpark
MetricsCollectorSparkTool
MetricsReadFilter
MetricsUtils
MinAlleleFractionFilter
MinibatchSliceSampler
MinimalGenotypingEngine
MinimalVariant
MinorAlleleFractionRecord
MinorAlleleFractionRecord.MinorAlleleFractionTableReader
MisencodedBaseQualityReadTransformer
MixingFraction
MMapBackedIteratorFactory
ModeledSegment
ModeledSegment.SimplePosteriorSummary
ModeledSegmentCollection
ModelSegments
Molten
MostDistantPrimaryAlignmentSelectionStrategy
MostDistantPrimaryAlignmentSelectionStrategy
MultiallelicFilter
MultiallelicSummary
MultiallelicSummary.Type
MultiDeBruijnVertex
MultidimensionalKernelSegmenter
MultidimensionalModeller
MultidimensionalSegment
MultidimensionalSegmentCollection
MultiHitAlignedReadIterator
MultiIntervalLocalReadShard
MultiIntervalShard
MultiLevelCollector
MultiLevelCollector
MultiLevelMetrics
MultilevelMetrics
MultiLevelReducibleCollector
MultiplePassVariantWalker
MultiSampleEdge
MultiTileBclFileFaker
MultiTileBclFileUtil
MultiTileBclParser
MultiTileFileUtil
MultiTileFilterParser
MultiTileLocsFileFaker
MultiTileLocsParser
MultiTileParser
MultiVariantDataSource
MultiVariantInputArgumentCollection
MultiVariantInputArgumentCollection.DefaultMultiVariantInputArgumentCollection
MultiVariantWalker
MultiVariantWalkerGroupedOnStart
Mutect2
Mutect2Engine
Mutect2FilteringEngine
Mutect2VariantFilter
MutectDownsampler
MutectReadThreadingAssemblerArgumentCollection
MutectStats
NativeUtils
NaturalLogUtils
NDNCigarReadTransformer
NestedIntegerArray
NestedIntegerArray.Leaf
NewIlluminaBasecallsConverter
NewIlluminaDataProvider
NGSPlatform
NioBam
NioFileCopierWithProgressMeter
NioFileCopierWithProgressMeter.ChecksumCalculator
NioFileCopierWithProgressMeter.Verbosity
NioFileCopierWithProgressMeterResults
NonChecksumLocalFileSystem
NonLocatableDoubleCollection
NonNFastaSize
NormalArtifactFilter
NormalizeFasta
NotOpticalDuplicateReadFilter
NovelAdjacencyAndAltHaplotype
NovelAdjacencyAndAltHaplotype.Serializer
Novelty
NRatioFilter
Nucleotide
Nucleotide.Counter
OjAlgoSingularValueDecomposer
OneBPIndel
OneShotLogger
OpticalDuplicateFinder
OpticalDuplicatesArgumentCollection
OptimizationUtils
OptionalFeatureInputArgumentCollection
OptionalIntervalArgumentCollection
OptionalReadInputArgumentCollection
OptionalReferenceArgumentCollection
OptionalReferenceInputArgumentCollection
OptionalVariantInputArgumentCollection
OrientationBiasFilterConstants
OrientationBiasFilterer
OrientationBiasFilterSummaryTableColumn
OrientationBiasReadCounts
OrientationBiasUtils
OrientationSampleTransitionSummary
OriginalAlignment
OtherProgramGroup
OutputMapping
OutputMode
OutputRenderer
OutputStreamSettings
OverclippedReadFilter
OverhangFixingManager
OverlappingErrorMetric
OverlappingReadsErrorCalculator
Pair
Pair
Pair.Serializer
PairedEnds
PairedStrandedIntervals
PairedStrandedIntervalTree
PairedStrandedIntervalTree.Serializer
PairedVariantSubContextIterator
PairedVariantSubContextIterator.VcfTuple
PairHMM
PairHMM.Implementation
PairHMMLikelihoodCalculationEngine
PairHMMLikelihoodCalculationEngine.PCRErrorModel
PairHMMModel
PairHMMNativeArgumentCollection
PalindromeArtifactClipReadTransformer
PanelMetricsBase
PanelOfNormalsFilter
ParallelCopyGCSDirectoryIntoHDFSSpark
Parameter
ParameterDecileCollection
ParameterEnum
ParameterizedFileUtil
ParameterizedModel
ParameterizedModel.GibbsBuilder
ParameterizedModel.UpdateMethod
ParameterizedState
ParameterSampler
ParameterTableColumn
ParamUtils
PartitionCrossingChecker
Passthrough
PassThroughDownsampler
Path
PathLineIterator
PathProvider
PathSeqBuildKmers
PathSeqBuildReferenceTaxonomy
PathSeqBwaSpark
PathSeqFilterSpark
PathSeqPipelineSpark
PathSeqScoreSpark
PathSpecifier
PathURI
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
PileupSummary.PileupSummaryComparator
PlatformReadFilter
PlatformUnitReadFilter
PloidyModel
PlotDenoisedCopyRatios
PlotModeledSegments
PolymeraseSlippageFilter
PolymorphicNuMTFilter
PosFileFaker
PosFileReader
PositionalDownsampler
PositionBasedDownsampleSam
PosParser
PossibleDeNovo
PosteriorProbabilitiesUtils
PosteriorProbabilitiesUtils.PosteriorProbabilitiesOptions
PosteriorSummary
PosteriorSummaryUtils
PostprocessGermlineCNVCalls
PowerCalculationUtils
PreAdapterOrientationScorer
PredicateFilterDecoratingClosableIterator
PreprocessIntervals
PrimaryAlignmentKey
PrimaryAlignmentKey
PrimaryAlignmentSelectionStrategy
PrimaryAlignmentSelectionStrategy
PrintBGZFBlockInformation
PrintMissingComp
PrintReads
PrintReadsSpark
PrintVariantsSpark
ProcessController
ProcessControllerAckResult
ProcessControllerBase
ProcessControllerBase.ProcessStream
ProcessOutput
ProcessSettings
ProgressLogger
ProgressMeter
ProgressReportingDelegatingCodec
PropertyUtils
ProteinChangeInfo
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
PushPullTransformer
PushToPullIterator
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
ReadBaseStratification
ReadBaseStratification.BinnedReadCycleStratifier
ReadBaseStratification.CigarOperatorsInReadStratifier
ReadBaseStratification.CollectionStratifier
ReadBaseStratification.Consensus
ReadBaseStratification.ConsensusStratifier
ReadBaseStratification.CycleBin
ReadBaseStratification.FlowCellTileStratifier
ReadBaseStratification.GCContentStratifier
ReadBaseStratification.IndelLengthStratifier
ReadBaseStratification.IndelsInReadStratifier
ReadBaseStratification.LongShortHomopolymer
ReadBaseStratification.LongShortHomopolymerStratifier
ReadBaseStratification.MismatchesInReadStratifier
ReadBaseStratification.NsInReadStratifier
ReadBaseStratification.PairOrientation
ReadBaseStratification.PairStratifier
ReadBaseStratification.ProperPaired
ReadBaseStratification.ReadDirection
ReadBaseStratification.ReadOrdinality
ReadBaseStratification.RecordAndOffsetStratifier
ReadCachingIterator
ReadClassifier
ReadClipper
ReadConstants
ReadContextData
ReadCoordinateComparator
ReadCovariates
ReadData
ReadDataManipulationProgramGroup
ReadDescriptor
ReadEnds
ReadEndsForMarkDuplicates
ReadEndsForMarkDuplicatesCodec
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.MateUnmappedAndUnmappedReadFilter
ReadFilterLibrary.NonChimericOriginalAlignmentReadFilter
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
ReadlessAssemblyRegion
ReadLikelihoodCalculationEngine
ReadLikelihoodCalculationEngine.Implementation
ReadMetadata
ReadMetadata.LibraryRawStatistics
ReadMetadata.LibraryRawStatistics.Serializer
ReadMetadata.PartitionBounds
ReadMetadata.PartitionBounds.Serializer
ReadMetadata.PartitionStatistics
ReadMetadata.PartitionStatistics.Serializer
ReadMetadata.Serializer
ReadNameEncoder
ReadNameParser
ReadNameReadFilter
ReadOrientation
ReadOrientationFilter
ReadPileup
ReadPosition
ReadPositionFilter
ReadPosRankSumTest
ReadQueryNameComparator
ReadRecalibrationInfo
ReadsContext
ReadsDataSource
ReadsDownsampler
ReadsDownsamplingIterator
ReadsForQNamesFinder
ReadsIterable
ReadsKey
ReadsKey.KeyForFragment
ReadsKey.KeyForPair
ReadsPipelineSpark
ReadsSparkSink
ReadsSparkSource
ReadStrandFilter
ReadStructure
ReadsWriteFormat
ReadThreadingAssembler
ReadThreadingAssemblerArgumentCollection
ReadThreadingGraph
ReadTransformer
ReadTransformerSparkifier
ReadTransformingIterator
ReadType
ReadUtils
ReadUtils.ClippingTail
ReadWalker
ReadWalkerContext
ReadWalkerSpark
RealignmentArgumentCollection
RealignmentEngine
ReblockGVCF
RecalDatum
RecalibrationArgumentCollection
RecalibrationReport
RecalibrationTables
RecalUtils
ReducibleAnnotation
ReducibleAnnotationData
ReferenceArgumentCollection
ReferenceBases
ReferenceBases
ReferenceConfidenceMode
ReferenceConfidenceModel
ReferenceConfidenceResult
ReferenceConfidenceUtils
ReferenceConfidenceVariantContextMerger
ReferenceConfidenceVariantContextMerger.VCWithNewAlleles
ReferenceContext
ReferenceDataSource
ReferenceFileSource
ReferenceFileSparkSource
ReferenceHadoopSparkSource
ReferenceInputArgumentCollection
ReferenceMemorySource
ReferenceMultiSparkSource
ReferenceProgramGroup
ReferenceShard
ReferenceSparkSource
ReferenceTwoBitSparkSource
ReferenceUtils
ReferenceWalker
ReferenceWindowFunctions
ReferenceWindowFunctions.FixedWindowFunction
RefFlatReader
RefFlatReader.RefFlatColumns
ReflectionUtil
RefVsAnyResult
RemoveNearbyIndels
RenameSampleInVcf
ReorderSam
ReplaceSamHeader
RepresentativeReadIndexer
RepresentativeReadIndexerCodec
RequiredFeatureInputArgumentCollection
RequiredIntervalArgumentCollection
RequiredReadInputArgumentCollection
RequiredReferenceArgumentCollection
RequiredReferenceInputArgumentCollection
RequiredStratification
RequiredVariantInputArgumentCollection
ReservoirDownsampler
Resource
RevertBaseQualityScores
RevertOriginalBaseQualitiesAndAddMateCigar
RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
RevertSam
RevertSam.FileType
RevertSamSpark
RevertSamSpark.FileType
RExecutor
RMSMappingQuality
RnaSeqMetrics
RnaSeqMetricsCollector
RnaSeqMetricsCollector.StrandSpecificity
RobustBrentSolver
RrbsCpgDetailMetrics
RrbsMetricsCollector
RrbsSummaryMetrics
RScriptExecutor
RScriptExecutorException
RScriptLibrary
RuntimeUtils
SamAlignmentMerger
SamAlignmentMerger
SamComparison
SamComparison
SamComparison.AlignmentComparison
SAMComparisonArgumentCollection
SamComparisonMetric
SAMFileDestination
SAMFileGATKReadWriter
SamFormatConverter
SAMPileupCodec
SAMPileupElement
SAMPileupFeature
Sample
Sample
SampleDB
SampleDBBuilder
SampleList
SampleList
SampleLocatableMetadata
SampleMetadata
SampleNameSplitter
SamplePairExtractor
SampleReadFilter
SamReaderQueryingIterator
SAMRecordAndReference
SAMRecordAndReference
SAMRecordAndReferenceMultiLevelCollector
SAMRecordAndReferenceMultiLevelCollector
SAMRecordMultiLevelCollector
SAMRecordMultiLevelCollector
SAMRecordSerializer
SAMRecordSparkCodec
SAMRecordToGATKReadAdapter
SAMRecordToGATKReadAdapterSerializer
SAMRecordToReadIterator
SamRecordWithOrdinalAndSetDuplicateReadFlag
SamToFastq
SamToFastqWithTags
SATagBuilder
ScatterIntervalsByNs
ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection
ScriptExecutor
ScriptExecutorException
SeekableByteChannelPrefetcher
SegmentedCpxVariantSimpleVariantExtractor
SegmentedCpxVariantSimpleVariantExtractor.ExtractedSimpleVariants
SegmentExonOverlaps
SegmentExonUtils
SelectVariants
SeqGraph
SequenceComparison
SequenceDictionaryUtils
SequenceDictionaryUtils
SequenceDictionaryUtils.SamSequenceRecordsIterator
SequenceDictionaryUtils.SequenceDictionaryCompatibility
SequenceDictionaryValidationArgumentCollection
SequenceDictionaryValidationArgumentCollection.NoValidationCollection
SequenceDictionaryValidationArgumentCollection.StandardValidationCollection
SequencerFlowClass
SequencingArtifactMetrics
SequencingArtifactMetrics.BaitBiasDetailMetrics
SequencingArtifactMetrics.BaitBiasSummaryMetrics
SequencingArtifactMetrics.PreAdapterDetailMetrics
SequencingArtifactMetrics.PreAdapterSummaryMetrics
SequencingError
SeqVertex
SerializableFunction
SetNmAndUqTags
SetNmMdAndUqTags
SetSizeUtils
Sex
Sex
Shard
ShardBoundary
ShardBoundaryShard
ShardedIntervalIterator
ShardToMultiIntervalShardAdapter
SharedSequenceMerger
SharedVertexSequenceSplitter
ShortVariantDiscoveryProgramGroup
SimpleAnnotatedIntervalWriter
SimpleChimera
SimpleChimera.DistancesBetweenAlignmentsOnRefAndOnRead
SimpleChimera.Serializer
SimpleCopyRatioCaller
SimpleCount
SimpleCountCollection
SimpleErrorCalculator
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.SupportedType
SimpleTsvOutputRenderer
SimpleXSVWriter
SingleBarcodeDistanceMetric
SinglePassSamProgram
SingleSequenceReferenceAligner
SingleSequenceReferenceAligner.TriFunction
SingularValueDecomposer
SliceSampler
SmithWatermanAligner
SmithWatermanAligner.Implementation
SmithWatermanAlignment
SmithWatermanIntelAligner
SmithWatermanJavaAligner
SmithWatermanJavaAligner.State
Snp
SnpEffPositionModifier
SnpEffPositionModifier.PositionModifier
SnpEffUtil
SnpEffUtil.EffectFunctionalClass
SnpEffUtil.EffectType
SoftClippedReadFilter
SomaticClusteringModel
SomaticGenotypingEngine
SomaticGVCFBlockCombiner
SomaticGVCFWriter
SomaticLikelihoodsEngine
SomaticReferenceConfidenceModel
SortableJexlVCMatchExp
SortSam
SortSamSpark
SortVcf
SparkCommandLineArgumentCollection
SparkCommandLineProgram
SparkContextFactory
SparkConverter
SparkSharder
SparkSingularValueDecomposer
SparkUtils
SplitIntervals
SplitNCigarReads
SplitReads
SplitSamByLibrary
SplitSamByNumberOfReads
SplitVcfs
StandardAnnotation
StandardArgumentDefinitions
StandardCallerArgumentCollection
StandardCovariateList
StandardEval
StandardHCAnnotation
StandardMutectAnnotation
StandardOptionDefinitions
StandardStratification
Strand
Strand.Serializer
StrandArtifactFilter
StrandArtifactFilter.EStep
StrandBiasBySample
StrandBiasTest
StrandCorrectedAllele
StrandCorrectedReferenceBases
StrandedInterval
StrandedInterval.Serializer
StrandOddsRatio
StrandSwitch
StratificationManager
StratificationManager.Combiner
Stratifier
StreamingProcessController
StreamingPythonScriptExecutor
StreamingToolConstants
StreamLocation
StreamOutput
StrictStrandBiasFilter
StripMateNumberTransformer
StructuralVariantDiscoveryProgramGroup
StructuralVariationDiscoveryArgumentCollection
StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigAlignmentsSparkArgumentCollection
StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection
StructuralVariationDiscoveryArgumentCollection.SvEvidenceFilterType
StructuralVariationDiscoveryPipelineSpark
StructuralVariationDiscoveryPipelineSpark.InMemoryAlignmentParser
SubsettedLikelihoodMatrix
SvCigarUtils
SVContext
SVD
SVDDenoisedCopyRatioResult
SVDDenoisingUtils
SVDFactory
SvDiscoverFromLocalAssemblyContigAlignmentsSpark
SvDiscoverFromLocalAssemblyContigAlignmentsSpark.AssemblyContigsClassifiedByAlignmentSignatures
SvDiscoverFromLocalAssemblyContigAlignmentsSpark.SAMFormattedContigAlignmentParser
SvDiscoverFromLocalAssemblyContigAlignmentsSpark.StructuralVariantFilter
SvDiscoverFromLocalAssemblyContigAlignmentsSpark.SVAlignmentLengthFilter
SvDiscoverFromLocalAssemblyContigAlignmentsSpark.SVMappingQualityFilter
SvDiscoveryInputMetaData
SvDiscoveryInputMetaData.ReferenceData
SvDiscoveryInputMetaData.SampleSpecificData
SvDiscoveryUtils
SVDReadCountPanelOfNormals
SVDUSTFilteredKmerizer
SVFastqUtils
SVFastqUtils.FastqRead
SVFastqUtils.FastqRead.Serializer
SVFastqUtils.Mapping
SVFileUtils
SVInterval
SVInterval.Serializer
SVInterval.SVIntervalConstructorArgsValidator
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
TandemRepeat
TargetedPcrMetrics
TargetedPcrMetricsCollector
TargetMetrics
TargetMetricsBase
TargetMetricsCollector
TargetMetricsCollector.Coverage
TemplateFragmentOrdinal
TensorType
Test
Testing
TestingReadThreadingGraph
TestProgramGroup
TextFormattingUtils
TextMDCodec
TextMDCodec.DeletionMDElement
TextMDCodec.MatchMDElement
TextMDCodec.MDElement
TextMDCodec.MismatchMDElement
TheoreticalSensitivity
TheoreticalSensitivity.RouletteWheel
TheoreticalSensitivityMetrics
ThetaVariantEvaluator
ThreadPoolExecutorUtil
ThreadPoolExecutorWithExceptions
ThresholdCalculator
ThresholdCalculator.Strategy
Tile
TileIndex
TileIndex.TileIndexRecord
TileMetricsOutReader
TileMetricsOutReader.IlluminaLaneTileCode
TileMetricsOutReader.IlluminaTileMetrics
TileMetricsOutReader.TileMetricsVersion
TileMetricsUtil
TilePhasingValue
TileTemplateRead
TiTvVariantEvaluator
TrainingSet
Tranche
Tranche.TrancheComparator
Tranche.TrancheTruthSensitivityComparator
TrancheManager
TrancheManager.SelectionMetric
TrancheManager.TruthSensitivityMetric
TranscriptSelectionMode
TransientFieldPhysicalLocation
Transition
Transition
Transition.Base
TraversalParameters
Trilean
Trio
TumorEvidenceFilter
TumorNormalPair
TwoPassFuncotationFilter
TwoPassReadWalker
TwoPassVariantWalker
TypeInferredFromSimpleChimera
UmiAwareMarkDuplicatesWithMateCigar
UmiGraph
UmiMetrics
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.MissingReferenceGziFile
UserException.NoSuitableCodecs
UserException.ReadMissingReadGroup
UserException.Require2BitReferenceForBroadcast
UserException.UnimplementedFeature
UserException.WrongFeatureType
Utils
ValidateBasicSomaticShortMutations
ValidateBasicSomaticShortMutations.Judgment
ValidateSamFile
ValidateSamFile.Mode
ValidateVariants
ValidateVariants.ValidationType
ValidationReport
VariantAccumulatorExecutor
VariantAccumulatorExecutor.MultiThreadedChunkBased
VariantAFEvaluator
VariantAnnotation
VariantAnnotator
VariantAnnotatorEngine
VariantAnnotatorEngine.VAExpression
VariantContextVariantAdapter
VariantDataManager
VariantEval
VariantEvalReportWriter
VariantEvaluationProgramGroup
VariantEvaluator
VariantEvalUtils
VariantFilter
VariantFilter
VariantFilteringProgramGroup
VariantFilterLibrary
VariantFilterLibrary.AllowAllVariantsVariantFilter
VariantFilterLibrary.NotSymbolicOrSVVariantFilter
VariantFilterLibrary.PassesFiltersVariantFilter
VariantFiltration
VariantIDsVariantFilter
VariantIteratorProducer
VariantLocusWalker
VariantManipulationProgramGroup
VariantOverlapAnnotator
VariantProcessor
VariantProcessor.Accumulator
VariantProcessor.AccumulatorGenerator
VariantProcessor.Builder
VariantProcessor.ResultMerger
VariantRecalibrator
VariantRecalibratorEngine
VariantShard
VariantsSparkSink
VariantsSparkSource
VariantsToTable
VariantStratifier
VariantSummary
VariantSummary.Type
VariantTransformer
VariantType
VariantType
VariantTypesVariantFilter
VariantWalker
VariantWalkerBase
VariantWalkerContext
VariantWalkerSpark
VcfFileSegment
VcfFileSegmentGenerator
VcfFormatConverter
VcfFuncotationFactory
VcfFuncotationMetadata
VcfOutputRenderer
VcfToAdpc
VcfToIntervalList
VcfUtils
VcfUtils
VectorLoglessPairHMM
VectorLoglessPairHMM.Implementation
VerifyIDIntensityContaminationMetrics
ViewSam
ViewSam.AlignmentStatus
ViewSam.PfStatus
ViterbiAlgorithm
VQSLODTranche
WalkerBase
WellformedReadFilter
WgsMetrics
WgsMetricsProcessor
WgsMetricsProcessorImpl
XGBoostEvidenceFilter
XReadLines
XsvLocatableTableCodec
XsvTableFeature