SingleContigRegionIterator
SingleSampleSingleAlleleEvidence
SkippableLocusKeyedIterator
SomaticAlternateReadDepthFilter
SomaticAverageBaseQualityFilter
SomaticAverageMappingQualityFilter
SomaticGenotypeFilterArguments
SomaticMedianMismatchFilter
SomaticMinimumLikelihoodFilter
sequenceIsAllStandardBases
somaticMaxGermlineErrorRatePercent
somaticNegativeLog10VariantPrior
somaticNegativeLog10VariantPriorRna
somaticNegativeLog10VariantPriorWithRnaEvidence
splitPartitionByContigAndMap