bedtools

Toolset for genome set arithmetic such as intersect, union

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.