BEDTools
Collectively, the BEDTools utilities are a swiss-army knife of tools for a wide range of genomics analysis tasks. They allow one to intersect, merge, count, complement and shuffle genomic intervals from multiple files in widely-used formats such as BED, GFF, GTF, VCF and BAM.
License
Free to use and open source under the MIT License.
Available
- Roihu: 2.31.1, via the
bio-appsmodule.
Usage
BEDTools is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the BEDTools module:
The utilities are run through the bedtools command followed by a subcommand. For
example, to find overlaps between two interval files:
Example batch script
#!/bin/bash
#SBATCH --job-name=bedtools
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=01:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=8G
module load bio-apps/v202603
module load bedtools2/2.31.1
bedtools intersect -a features.bed -b regions.bed > overlaps.bed
Replace <project> with your CSC project (for example project_2001234).
See creating a batch job script for Roihu for more information about running batch jobs.