BEDTools

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

Usage on Bridges-2

To see what versions of BEDTools are available and if there is more than one, which is the default, along with some help, type

module spider bedtools

To use ABySS, include a command like this in your batch script or interactive session to load the ABySS module: (note ‘module load’ is case-sensitive):

module load bedtools

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.

 

See more help on BEDTools