Estimating background mutation rates from MutSig (Broad Institute)
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9.8 years ago
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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?

MutSig BMR • 3.0k views
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