coverage confusion in mutSig. Why there are covered bases with categ=7 and effect="silent/noncoding"
Dear Mutsig Developers,
I am trying to understand the algorithm more.
I used the coverage file from the TCGA Lung Squamous paper provided from the mutSig website. However, the file really confuses me. When I do a cross tabulation, there are many bases with categ = 7 and effect = "silent" or "noncoding". This doesn't make sense to me because I thought all the 7th category (null mutation) should necessarily fall in the coding region and have a non-silent effect (which is true for the maf file). Could someone explain this a little?
Thanks a lot.