How To Find Cnvs Common To Both Of The Responders (Overlapping Regions) From Varscan Output

Question

[sousuffer]

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!

Answer 1

[Anthony Mathelier]

If you convert your files into bed files, then you can use the bedtools at http://code.google.com/p/bedtools/ to intersect your files.