bedtools
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
Documentation
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.
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 small,large,ram256g,ram1t
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
Mangi Modules
Default
2.29.2
Other Modules
2.17.0, 2.25.0, 2.27.1, 2.29.2
Mesabi Modules
Default
2.29.2
Other Modules
2.17.0, 2.25.0, 2.27.1, 2.29.2