Calculate reciprocal overlap for thousands of samples

Question

[QVINTVS_FABIVS_MAXIMVS]

I have around 20k samples with BED files. How can I calculate reciprocal overlap for each segment? I want to find all segments with 50% reciprocal overlap or better.

Answer 1

[ebrown1955]

You can use bedtools intersect for this. http://bedtools.readthedocs.org/en/latest/