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. While each individual tool is designed to do a relatively simple task, quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.

Availability and Restrictions


The following versions of bedtools are available on OSC clusters:

Version Owens
2.25.0 X
2.29.2 X*
* Current default version

You can use module spider bedtools to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.


bedtools is available to all OSC users. If you have any questions, please contact OSC Help.

Publisher/Vendor/Repository and License Type

Aaron R. Quinlan and Neil Kindlon, Open source


Usage on Owens


To configure your environment for use of bedtools, run the following command: module load bedtools. The default version will be loaded. To select a particular bedtools version, use module load bedtools/version. For example, use module load bedtools/2.25.0 to load bedtools 2.25.0.

Further Reading

Fields of Science: