org.hammerlab.guacamole.commands

GermlineAssemblyCaller

object GermlineAssemblyCaller

Simple assembly based germline variant caller

Overview: - Find areas where > min-area-vaf % of the reads show a variant - Place the reads in the snv-window-range-base window into a DeBruijn graph and find paths between the start and end of the reference sequence that covers that region - Align those paths to the reference sequence to discover variants

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  1. class Arguments extends Args4jBase with GermlineCallerArgs with AssemblyArgs with PartitionedRegionsArgs with ReferenceArgs

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  1. final def !=(arg0: AnyRef): Boolean

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  6. object Caller extends SparkCommand[Arguments] with GenotypeOutputCaller[Arguments, CalledAllele]

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  11. def finalize(): Unit

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  12. final def getClass(): Class[_]

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  14. final def isInstanceOf[T0]: Boolean

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  16. final def notify(): Unit

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  17. final def notifyAll(): Unit

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  18. final def synchronized[T0](arg0: ⇒ T0): T0

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