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Purity adjustments for CNV calls from the GATK-CNV Firecloud pipeline
Hi Firecloud/GATK team!
We are really enjoying using the CNV pipeline in Firecloud - so far it's giving us some of the cleanest calls we've seen and the "extras" (like figures, baf, etc.) are all great!
One question that we had was, does this pipeline adjust its calls for the purity of the sample?
Put a different way, the question could be "if we wanted to make cnv calls beyond +/-, like +1, +2, -1, -2, would we need to adjust the copy number ratio from this pipeline for purity, or has that already been done, and we could, say, just set a threshold that we felt comfortable with and it would be broadly applicable across samples?"