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
Source

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