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  • 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.

  • Usage

    To list all executables provided by bedtools, run: $ sbgrid-list bedtools Copy to clipboard
  • Installation

    Use the following command to install this title with the CLI client: $ sbgrid-cli install bedtools Copy to clipboard Available operating systems: Linux 64, OS X INTEL
  • 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:  2.31.1 (23.4 MB)
    OS X INTEL:  2.31.1 (12.8 MB)

  • Other Versions

      Linux 64:

      2.26.0 (1.9 MB) , 2.29.0 (55.5 MB) , 2.30.0 (69.6 MB) , 2.31.0 (22.8 MB)
    • OS X INTEL:

      2.26.0 (2.1 MB) , 2.29.0 (3.9 MB) , 2.30.0 (11.9 MB) , 2.31.0 (12.7 MB)
  • Developers

    Aaron R Quinlan