b) What does (......) mean?
Forwarding this along as a colleague asked me about this and it seemed odd to me. She was able to enter a ploidy argument in Mutect2, and what wondering what effect it has. I checked the documentation, and sure enough, I saw that ploidy was listed as a valid argument with a default of 2. I want to guess that this argument may not actually be used, even if entered, and may be a "vestigial" argument from the HC engine. If ploidy is used, what should be used for samples looking at viral variation in a composite sample or mitochondrial variation within a tissue sample?
Please sign in to leave a comment.