Matching genomic regions / Intersect BED


Reports overlaps between two feature files such as BED, VCF and GTF. One of the files can also be BAM. Note that when A and B files are compared, the B file is loaded into memory. Therefore to minimize memory usage, one should set the smaller of the two files as the B file.



By far, the most common question asked of two sets of genomic features is whether or not any of the features in the two sets “overlap” with one another. This is known as feature intersection. IntersectBed allows one to screen for overlaps between two sets of genomic features. Moreover, it allows one to have fine control as to how the intersections are reported. IntersectBed works with both BED/GFF/VCF and BAM files as input.


The output is a tab-delimited text 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. 841–842.

Please see the BEDTools homepage for more details.