I usually use bedtools intersect
to find overlapping regions of bed files, but it seems like this tool can only output overlap between a pair of files. I need something that can do the following from many bed files and only report regions contained in all of the bed files.
Example input from 4 separate bed files:
chr1 50 100
chr1 60 120
chr1 30 90
chr1 50 90
Desired output:
chr1 60 90
Any tools for this? Maybe I should just cat
all the bed files together and merge them?