Bedtools

Introduction

Bedtools is an extensive suite of utilities for genome arithmetic and comparing genomic features in BED format.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/bedtools
Home page: https://github.com/arq5x/bedtools2

Versions

  • 2.30.0

  • 2.31.0

Commands

  • annotateBed

  • bamToBed

  • bamToFastq

  • bed12ToBed6

  • bedpeToBam

  • bedToBam

  • bedToIgv

  • bedtools

  • closestBed

  • clusterBed

  • complementBed

  • coverageBed

  • expandCols

  • fastaFromBed

  • flankBed

  • genomeCoverageBed

  • getOverlap

  • groupBy

  • intersectBed

  • linksBed

  • mapBed

  • maskFastaFromBed

  • mergeBed

  • multiBamCov

  • multiIntersectBed

  • nucBed

  • pairToBed

  • pairToPair

  • randomBed

  • shiftBed

  • shuffleBed

  • slopBed

  • sortBed

  • subtractBed

  • tagBam

  • unionBedGraphs

  • windowBed

  • windowMaker

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run bedtools on our clusters:

#!/bin/bash
#SBATCH -p PartitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 4
#SBATCH --mem=8G
#SBATCH --job-name=bedtools
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module purge
module load bedtools/XXXX ### you can run *module avail bedtools* to check all available versions

bedtools intersect -a a.bed -b b.bed
bedtools annotate -i variants.bed -files genes.bed conserve.bed known_var.bed