Bedtools
Introduction
Bedtools
is an extensive suite of utilities for genome arithmetic and comparing genomic features in BED format.
For more information, please check its website: https://biocontainers.pro/tools/bedtools and its home page on Github.
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
Module
You can load the modules by:
module load biocontainers
module load bedtools
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 -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=bedtools
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers bedtools
bedtools intersect -a a.bed -b b.bed
bedtools annotate -i variants.bed -files genes.bed conserve.bed known_var.bed