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
chr1 60 90
Any tools for this? Maybe I should just
cat all the bed files together and merge them?