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Hierarchy For Package org.broadinstitute.hellbender.tools.walkers.annotator
Package Hierarchies:
All Packages
Class Hierarchy
java.lang.Object
org.broadinstitute.hellbender.tools.walkers.annotator.
AnnotationUtils
org.broadinstitute.hellbender.cmdline.
CommandLineProgram
(implements org.broadinstitute.barclay.argparser.CommandLinePluginProvider)
org.broadinstitute.hellbender.engine.
GATKTool
org.broadinstitute.hellbender.engine.
VariantWalkerBase
org.broadinstitute.hellbender.engine.
VariantWalker
org.broadinstitute.hellbender.tools.walkers.annotator.
VariantAnnotator
org.broadinstitute.hellbender.tools.walkers.annotator.
HeterozygosityCalculator
org.broadinstitute.hellbender.tools.walkers.annotator.
VariantAnnotation
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
Annotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
GenotypeAnnotation
org.broadinstitute.hellbender.tools.walkers.annotator.
DepthPerAlleleBySample
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardAnnotation
, org.broadinstitute.hellbender.tools.walkers.annotator.
StandardMutectAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
DepthPerSampleHC
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardHCAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
OxoGReadCounts
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardMutectAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
PerAlleleAnnotation
org.broadinstitute.hellbender.tools.walkers.annotator.
BaseQuality
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardMutectAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
FragmentLength
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardMutectAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
MappingQuality
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardMutectAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
ReadPosition
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardMutectAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
StrandArtifact
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardMutectAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
StrandBiasBySample
org.broadinstitute.hellbender.tools.walkers.annotator.
UniqueAltReadCount
org.broadinstitute.hellbender.tools.walkers.annotator.
InfoFieldAnnotation
org.broadinstitute.hellbender.tools.walkers.annotator.
ChromosomeCounts
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
Coverage
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardAnnotation
, org.broadinstitute.hellbender.tools.walkers.annotator.
StandardMutectAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
GenotypeSummaries
org.broadinstitute.hellbender.tools.walkers.annotator.
MappingQualityZero
org.broadinstitute.hellbender.tools.walkers.annotator.
PedigreeAnnotation
org.broadinstitute.hellbender.tools.walkers.annotator.
ExcessHet
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
InbreedingCoeff
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
PossibleDeNovo
org.broadinstitute.hellbender.tools.walkers.annotator.
QualByDepth
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
RankSumTest
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
Annotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
BaseQualityRankSumTest
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
ClippingRankSumTest
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardHCAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
LikelihoodRankSumTest
org.broadinstitute.hellbender.tools.walkers.annotator.
MappingQualityRankSumTest
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
ReadPosRankSumTest
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
ReferenceBases
org.broadinstitute.hellbender.tools.walkers.annotator.
RMSMappingQuality
(implements org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.
ReducibleAnnotation
, org.broadinstitute.hellbender.tools.walkers.annotator.
StandardAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
SampleList
org.broadinstitute.hellbender.tools.walkers.annotator.
StrandBiasTest
org.broadinstitute.hellbender.tools.walkers.annotator.
FisherStrand
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
StrandOddsRatio
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
TandemRepeat
(implements org.broadinstitute.hellbender.tools.walkers.annotator.
StandardMutectAnnotation
)
org.broadinstitute.hellbender.tools.walkers.annotator.
VariantAnnotatorEngine
org.broadinstitute.hellbender.tools.walkers.annotator.
VariantAnnotatorEngine.VAExpression
org.broadinstitute.hellbender.tools.walkers.annotator.
VariantOverlapAnnotator
Interface Hierarchy
org.broadinstitute.hellbender.tools.walkers.annotator.
Annotation
org.broadinstitute.hellbender.tools.walkers.annotator.
StandardAnnotation
org.broadinstitute.hellbender.tools.walkers.annotator.
StandardHCAnnotation
org.broadinstitute.hellbender.tools.walkers.annotator.
StandardMutectAnnotation
Enum Hierarchy
java.lang.Object
java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
org.broadinstitute.hellbender.tools.walkers.annotator.
StrandArtifact.ArtifactState
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