Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.

While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.

Documentation

User Guide
Cheatsheet

Slurm script

#!/bin/bash
#SBATCH --job-name=bedtools
#SBATCH --time=1:00:00
#SBATCH --partition=norm
#SBATCH --ntasks=1
#SBATCH --mem=64GB
module load bedtools
# bedtools sorted
bedtools intersect -a ccds.exons.bed -b aln.bam.bed -c -sorted
# bedtools unsorted
bedtools intersect -a ccds.exons.bed -b aln.bam.bed -c
# bedmap (without error checking)
bedmap --echo --count --bp-ovr 1 ccds.exons.bed aln.bam.bed
# bedmap (no error checking)
bedmap --ec --echo --count --bp-ovr 1 ccds.exons.bed aln.bam.bed