Matching genomic regions / Subtract BED


Removes the portion(s) of an interval that is overlapped by another feature(s).



subtractBed searches for features in B that overlap A. If an overlapping feature is found in B, the overlapping portion is removed from A and the remaining portion of A is reported. If a feature in B overlaps all of a feature in A, the A feature will not be reported.


The output is a BED file.


This tool uses the BEDTools package. Please cite the article:

Quinlan AR and Hall IM, 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 26, 6, pp. 841842.

Please see the BEDTools homepage for more details.