finding novel CNVs

Question

[mw848]

I have an excel file that consist of 48 separate tumor samples and one control with hundreds of coordinates that have chromosomal losses or gains. I would like to find overlapping coordinates between samples to find novel copy number alterations among the samples. What is the best way to go about this?

Answer 1

[Pierre Lindenbaum]

export to a BED file and use "bedtools intersect" with a BED of known CNVs with option '-r'.

Require that the fraction of overlap be reciprocal for A and B. In other words, if -f is 0.90 and -r is used, this requires that B overlap at least 90% of A and that A also overlaps at least 90% of B.

[mw848]

Hi Pierre, Thank you for your quick response. The excel file I have already has a list of called CNVs and their chromosomal positions. I just want to tally up which samples have the same coordinate (overlapped coordinates) loss or gains. Do I need to compare this BED file to a known CNV BED file that I can find online?