- CannotAnnotateMendelianInheritance
- CannotTranslateHGVSVariant
- ConsumerProcessor
- CoordinateSortingChecker
- GeneWiseMendelianAnnotationProcessor
- GenomeRegion
- GenomeRegionList
- GenomeRegionListFactoryFromSAMSequenceDictionary
- GenomeRegionSequenceExtractor
- InvalidBreakendDescriptionException
- InvalidCoordinatesException
- MendelVCFHeaderExtender
- MissingEndInfoField
- MissingSVTypeInfoField
- MixingSmallAndSVAlleles
- MultipleSVAlleles
- NucleotideChangeToGenomeVariantTranslationImplBase
- NucleotideChangeToGenomeVariantTranslator
- NucleotideLocationConverter
- ProgressReporter
- VariantContextAnnotator
- VariantContextAnnotator.Options
- VariantContextCounter
- VariantContextFilterException
- VariantContextMendelianAnnotator
- VariantContextProcessor
- VariantContextWriterConstructionHelper
- VariantEffectHeaderExtender