unmappedBam

CreateUnmappedBamFromFastqPipeline DnaResequencingFromUnmappedBamPipeline

useBwaBacktrack

DnaResequencingFromFastqPipeline DnaResequencingFromUnmappedBamPipeline

useGatk

GermlineVariantCallingPipeline

useNativePairHmm

ParallelHaplotypeCaller