BeagleOutputToVCF
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CallableLoci
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CheckPileup
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ClipReads
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CompareCallableLoci
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CountBases
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CountIntervals
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CountLoci
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CountMales
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CountReadEvents
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CountRODs
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CountRODsByRef
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CountTerminusEvent
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CoveredByNSamplesSites
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DepthOfCoverage
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DiagnoseTargets
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DiffObjects
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ErrorRatePerCycle
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FastaAlternateReferenceMaker
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FastaReferenceMaker
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FastaStats
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FilterLiftedVariants
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FindCoveredIntervals
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FlagStat
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GCContentByInterval
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GenotypeAndValidate
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HaplotypeResolver
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Pileup
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PrintRODs
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ProduceBeagleInput
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QCRef
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QualifyMissingIntervals
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RandomlySplitVariants
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ReadAdaptorTrimmer
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ReadClippingStats
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ReadGroupProperties
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ReadLengthDistribution
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RegenotypeVariants
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SelectHeaders
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SimulateReadsForVariants
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SplitSamFile
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ValidateVariants
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ValidationSiteSelector
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VariantsToBeagleUnphased
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VariantValidationAssessor
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