Find consensus overlap between many bed files

Question

[goodez]

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?

Answer 1

[Alex Reynolds]

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.

[goodez]

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.

[Alex Reynolds]

bedops --intersect will give you the answer you want without additional steps.

[goodez]

Thanks it was just one pipe to awk using bedtools, but I'm going to switch to bedops. +1 for every answer lol they're all good

[rohitsatyam102]

I agree. I used the bedops --intersect and it has same functionality as bedtools multiinter and you won't require even filtering.

Answer 2

[venu]

Maybe I should just cat all the bed files together and merge them?

You can do that. But there is also multiIntersect. Check here

[goodez]

Thanks! My servers at work had multiIntersectBed already installed, which I guess is also known as bedtools multiinter as genomax suggested. This is just the functionality I was looking for, nothing fancy, just common regions between many bed files.

Answer 3

[GenoMax]

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.

[goodez]

Thanks to you and venu for pointing me in the right direction. +1 for both