org.hammerlab.guacamole.commands

SomaticStandard

object SomaticStandard

Simple subtraction based somatic variant caller

This takes two variant callers, calls variants on tumor and normal independently, and outputs the variants in the tumor sample BUT NOT the normal sample.

This assumes that both read sets only contain a single sample, otherwise we should compare on a sample identifier when joining the genotypes

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

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