So I have a pretty simple question that I actually can't seem to be able to figure out. So far I have been using bedtools to find overlaps between two bed files using intersectBed. Example:

```
Bed A
Bed B
Bed C
```

Now I have three generated bed files that I want to overlap to find peaks/regions common among all three.

    ABC

The multiintersect option doesn't seem to have any documentation besides the information found here https://www.biostars.org/p/13516/ but the function itself doesn't seem to give me the information I'm looking for. Specifically I want to feed in three bed files and find only the common regions between ALL three, not AB, AC, BC, and ABC in one large file which seems to be the output shown in the linked example.

I believe that `intersectBed -a A -b B C` does something similar to the above, but perhaps I'm simply running it wrong and my attempts are errors on my part.

Can this be done using bedtools? If not, what other similar software is out there that can accomplish this?

I appreciate any help,

Carlos
Answer:

First find in-between any two files and use the results to compare with third file.

    intersectBed -a 1.bed -b 2.bed | intersectBed -a - -b 3.bed