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Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome.

For example, 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. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.

bedtools is developed in the Quinlan laboratory at the University of Utah and benefits from fantastic contributions made by scientists worldwide.

How to use

Check for available versions of bedtools:

$ module avail bedtools

We recommend using the latest version.

Always load a module for specific version. Example:

$ module load bedtools/2.28.0

This will add the directory containing the binaries to your PATH. For more details on using modules see our software applications guide.

Authors: Javed Shaikh, Mohsin Ali
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