Kurt-Hetrick / CIDR_SOMATIC_WES_PIPELINES

currently for paired tumor - normal WES samples processed with TWIST UMIs
MIT License
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add gatk getpileupsummaries and calculatecontamination #13

Closed Kurt-Hetrick closed 1 year ago

Kurt-Hetrick commented 1 year ago

might help determine with tumor cellularity

using gnomad frequencies for now. if computationally too intensive on exomes can look into switching to exac. after a couple of tests on a small capture, they were reasonably close to within a percent.

Kurt-Hetrick commented 1 year ago

done for qc pipeline