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The Bedtools suite is a collection of tools for a wide-range of genomics analysis tasks.

Bedtools is available as a module on Apocrita.


To run the default installed version of Bedtools, simply load the bedtools module:

$ module load bedtools
$ bedtools -h

Usage:   bedtools <subcommand> [options]

For full usage documentation, run bedtools -h.

Example job

Serial job

Here is an example job running on 1 core and 1GB of memory:

#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load bedtools

# Report the base-pair overlap between the features in two BED files.
bedtools intersect -a reads.bed -b genes.bed