bedtools

Summary

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