Supported Applications


  • Description

    a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic. 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, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.

  • Primary Citation*

    A. R. Quinlan and I. M. Hall. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 26(6): 841-842.

    • *Full citation information available through

  • Keywords


  • Default Versions

    Linux 64:  2.26.0
    OS X INTEL:  2.26.0

  • Developers

    Aaron Quinlan.