Estimating background mutation rates from MutSig (Broad Institute)
I recently ran MutSigCV (broad institute package) on a .maf file from TCGA data specifically to get an estimate of background mutation rate (BMR). There are output files for mutations and for significant genes, I'm assuming that the n_silent from the latter is the proxy estimate for background mutation rate (i.e. silent substitution rate), or is it some other field in this or the mutation output file?
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