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.
Documentation
- 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).
Usage on Bridges
To see what other modules are needed, what commands are available and how to get additional help type
module help bedtools
To see what versions of BEDtools are available type
module avail bedtools
To use BEDtools, include a command like this in your batch script or interactive session to load the BEDTools module:
module load bedtools
Be sure you also load any other modules needed, as listed by the module help bedtools command.
Usage on BioU
The BEDTools programs are available through the Galaxy instance on biou.
To make the BEDTools programs available through the command line, csh users should enter the following command:
source /packages/bin/SETUP_BIO_SOFTWARE
To make the BEDTools programs available through the command line, bash users should enter the following command:
source /packages/bin/SETUP_BIO_SOFTWARE
