change haplotype caller contamination adjustment from freemix to gatk tumor contam

Kurt-Hetrick / CIDR_SOMATIC_WES_PIPELINES

currently for paired tumor - normal WES samples processed with TWIST UMIs

MIT License

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Open Kurt-Hetrick opened 1 year ago

Kurt-Hetrick commented 1 year ago

seems like that would be the better way to go. need to test normal mixed samples first.

Kurt-Hetrick commented 9 months ago

hmmm. now i wonder if i actually want to do this...i guess if the goal is to achieve higher concordance with array data, then the answer is yes.