I tried testing MuSiC (v0.4) but have gotten substantially more significantly mutated genes then expected. For my own pan-cancer dataset it returned thousands of genes, and for a testing set of published Ovarian somatic mutations returned ~350. I used the default settings for these runs using
smg (so I didn't need the BAM files). I obtained the ovarian MAF file from synapse (https://www.synapse.org/#!Synapse:syn1729383 ), coverage wig files from firehose (recommended on this post), and recommended ROI file (here). Is there anything I'm missing or are there parameter tweaks or changes so MuSiC reports a more reasonable number of significantly mutated genes?
I saw a couple of parameters that might be helpful. One was the
--bmr-groups option in
genome music bmr calc-bmr, which appears to group samples into a certain number of similarly mutated groups. Is there a recommended way to set up the number of BMR groups? Another was the
--bmr-modifier-file option in
genome music smg as a multiplication factor for the background mutation rate for certain genes. Is there a standard/recommended BMR modifier file?