I have used VarScan to identify CNVs in whole exome data using tumor and matching normal. I have four patients - two that respond to treatment, and two that do not. We are looking for CNVs common to the responders and not contained by the non-responsive patients (and vice versa).
I have four output files in the following format:
chrom loc.start loc.end num.mark seg.mean chr1 126901 336305 20 -0.2205 chr1 566191 569388 3 1.2087 chr1 653310 2338123 1505 -0.1378 chr1 2338223 16057066 5079 -0.19
I am trying to find CNVs common to both of the responders (overlapping regions) and was wondering if there are any existing tools that can do this? Any help would be greatly appreciated!