julianhess

Hi, This is coming from an issue with coverage_basewise.fwb/coverage_basewise.fwi. Is it possible that these files are not being specified properly (or corrupted)? —Julian

A few things to consider: * Is the MAF completely clean of artifacts? * Are the samples fresh frozen? FFPE? * Is there potential germline contamination in the MAF? *...

Did you download the reference files from [here](http://software.broadinstitute.org/cancer/cga/sites/default/files/data/tools/mutsig/MutSig2CV.tar.gz)?

Hi,Looks like your MAF is malformed—there seem to be blank chromosomes, and a chromosome named “Chromosome,” suggesting that multiple TSVs have been catted together without removing headers in between.The newbase...

Can you please post an excerpt of your MAF? Sounds like there are some other problems with the mutation data.