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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.


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

module load bedtools

See more help on BEDTools