BEDTools is a collection of utilities for comparing, summarizing, and intersecting genomic features in the UCSC Genome Browser BED format. BEDTools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.
- Website: http://code.google.com/p/bedtools/
- Manual: http://bedtools.readthedocs.org/en/latest/
- AR Quinlan and IM Hall, BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 26 (6): 841–842 (2010).