Merging CNV data with Mutation data and running on MutSigCV

I am trying to find the most significant altered genes and I was thinking of using only 1 tool for significance test which is MutSigCV instead of MutSigCV for mutation data and GISTIC for CNV data. I know that MutSigCV works with short indels but can I merge my CNV segmented data in the MAF file (Divide each long CNV into regions) and input them to MutSigCV or this wouldn't work? Can MutSigCV work with long insertions or deletions? What is the maximum indel length that MutSigCV can operate on?