MutSigCV - Not enough mutations to analyze

ioantikaioantika Member
edited February 28 in Ask the GATK team

I am running MutSigCV on GP in order to extrapolate significantly mutated genes in a cohort of 249 ovarian cancer FFPE samples after claiming 14472 mutations with targeted IonTorrent AmpliSeq on driver genes. I have used the full coverage for the first run provided that I want to fill out my MAF file with mutation categories and optimize my coverage file according to them before running the official final analysis. The completed analysis points out an error and the output contains a little less than 100 mutations annotated with categories (C->T, *ApA->mut, etc.), while the following message is provided in stderr;

Error using gp_MutSigCV>MutSig_runCV (line 850)
not enough mutations to analyze

Error in gp_MutSigCV (line 194)



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