The bedtools utilities are a suite of tools for performing a wide
range of genomics analysis tasks.  The most widely-used of these
tools enable genome arithmetic, i.e., set theory on the genome.
For example, with bedtools one can intersect, merge, count,
complement, and shuffle genomic intervals from multiple files in
common genomic formats such as BAM, BED, GFF/GTF, and VCF.

Although each individual utility is designed to do a relatively
simple task, e.g., intersect two interval files, more sophisticated
analyses can be conducted by stringing together multiple bedtools
operations on the command line or in shell scripts.