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Warning!

Puhti and Mahti computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti and Mahti login nodes and storage services are planned to remain available until 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

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-apps module.

Usage

BEDTools is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the BEDTools module:

module load bio-apps/v202603
module load bedtools2/2.31.1

The utilities are run through the bedtools command followed by a subcommand. For example, to find overlaps between two interval files:

bedtools intersect -a features.bed -b regions.bed > overlaps.bed

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.

Support

CSC Service Desk

More information