Question about Copy-Number Data produced using Sequenza
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5.3 years ago

I have a list of mutations and want to filter out mutations that are non-diploid or have been amplified or deleted.

The data I'm working with had mutations called using MuTect and copy-number data produced using Sequenza.

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

R copy-number Sequenza • 2.2k views
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