# bedtools

## Summary

+ **Module Name:** bedtools
+ **Support Level:** Primary Support
+ **Software Access Level:** Open Access
+ **Home Page:** [http://bedtools.readthedocs.io/en/latest/](http://bedtools.readthedocs.io/en/latest/)

## Software Description

The BEDTools utilities allow one to address common genomics tasks such
as finding feature overlaps and computing coverage. The utilities are
largely based on four widely-used file formats: BED, GFF/GTF, VCF, and
SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that
answer complicated research questions by \"streaming\" several BEDTools
together.
## General Linux

To load this module for use in a Linux environment, you can run the command:

	module load bedtools

Depending on where you are working, there may be more than one version of bedtools available.
To see which modules are available for loading you can run:

	module avail bedtools
## Slurm Example


	#!/bin/bash
	#SBATCH --job-name="rfm_RunBedToolTest_job"
	#SBATCH --ntasks=1
	#SBATCH --ntasks-per-node=1
	#SBATCH --output=rfm_RunBedToolTest_job.out
	#SBATCH --error=rfm_RunBedToolTest_job.err
	#SBATCH --time=0:10:0
	#SBATCH -p msismall
	module load bedtools/2.29.2
	wget https://public.s3.msi.umn.edu/reframe/sw/bedtools/out.bam
	bedtools bamtobed -i out.bam