bedtools

Genetics

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.


Info

Module Name

bedtools

Last Updated On

08/29/2023

Support Level

Primary Support

Software Access Level

Open Access

Home Page

http://bedtools.readthedocs.io/en/latest/

Documentation

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

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

Agate Modules

Default

2.29.2

Other Modules

2.17.0, 2.25.0, 2.27.1, 2.29.2