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?
To intersect intervals from 1 to N files, simply use bedops --intersect:
$ bedops --intersect A.bed B.bed ... N.bed > answer.bed
More details from the documentation: http://bedops.readthedocs.io/en/latest/content/reference/set-operations/bedops.html#intersect-i-intersect
This requires sorted BED files. You can use BEDOPS sort-bed to do this quickly.
I think the other toolkit suggestions now require sorted BED files, as well.
I was able to find all overlapping regions of my BEDs using bedtools multiinter, although I had to filter the output to only keep regions found in all BEDs.
I'll try out bedops --intersect too since the output might be easier to keep in my pipeline. To sort the BEDs, I found bedtools sort worked great.
bedops --intersect will give you the answer you want without additional steps.
I agree. I used the bedops --intersect and it has same functionality as bedtools multiinter and you won't require even filtering.
Intersect multiple BED files (bedops option)
There is also
bedtools multiinter
Tool: bedtools multiinter (aka multiIntersectBed)
Version: v2.26.0
Summary: Identifies common intervals among multiple
BED/GFF/VCF files.
Usage: bedtools multiinter [OPTIONS] -i FILE1 FILE2 .. FILEn
Requires that each interval file is sorted by chrom/start.
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