Compare a long list of BEDFiles against a whole genome/ chromosome ?

Question

[dearbbhyc]

Do you think it is possible for me to compare a list of BEDFiles against a whole genome or even chromosome? If so, How?

I am trying to compare a list of chromosomal regions to a whole genome CNV map and then count the number of gains and losses in these regions.

Hope someone can help.

[Pierre Lindenbaum]

the answer is bedtools

[GenoMax]

Bedtools can be found here.

Answer 1

[Alex Reynolds]

You could use bedmap to count overlapping elements, e.g. to count the number of elements in B that overlap regions in A:

$ bedmap --echo --count A.bed B.bed > answer.bed

Full documentation is available here: http://bedops.readthedocs.io/en/latest/content/reference/statistics/bedmap.html