MutSigCV coverage file

Dear MutSigCV Developers,
I have noticed that the coverage file provided by Genepattern is an "exome" file. Does the exome mean CDS + UTR for each gene? So, should I remove the mutations on intron before running MutSigCV, because intronic coverage data are not included in the coverage file (not considered when calculating N_noncoding)?
And is it reasonable to use only CDS mutations and change the coverage of all noncoding categs to zero?