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?
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.