I have a list of mutations and want to filter out mutations that are non-diploid or have been amplified or deleted.
I do not have access to the raw sequencing data so I can't re-run the analysis; I can only interpret the available data.
The MuTect data tells me how the variant allele frequency for each mutation. The Sequenza data tells me a "seg.mean" value for pretty much every mutation (once I matched the coordinates from the two output files). What I'm trying to figure out is how I can combine these values to filter my list to only diploid mutations which haven't been amplified or deleted. If "seg.mean" means the same thing as "copy-number log ratio mean" I would probably just filter using so that:
-0.5 <= seg.mean <= 0.5
P.S. It HAS occurred to me that I might want to use purity-corrected values; I've got purity measures based on histology rather than sequencing data