Matching genomic regions / Overlap BEDPE with BED


Report overlaps between a BEDPE file and a BED/GFF/VCF file.



pairToBed compares each end of a BEDPE feature or a paired-end BAM alignment to a feature file in search of overlaps.

NOTE: pairToBed requires that the BAM file is sorted/grouped by the read name. This allows pairToBed to extract correct alignment coordinates for each end based on their respective CIGAR strings. It also assumes that the alignments for a given pair come in groups of twos. There is not yet a standard method for reporting multiple alignments using BAM. pairToBed will fail if an aligner does not report alignments in pairs.

Selecting "File A is BAM format [yes]" is analogous to using "-abam" option instead of "-a" in the command line version.


The output is either a BEDPE file or a compressed or uncompressed BAM file depending on input file and options selected.


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.