bedtools

BEDTools is a free, open-source collection of command-line utilities designed for genome arithmetic—manipulating and comparing features represented as intervals on a reference genome. It is widely used to analyze and annotate genomic features such as genes, exons, peaks, and variants, enabling researchers to perform routine interval operations efficiently.

The toolkit provides core operations such as intersect, merge, subtract (complement), and union, as well as functions for proximity queries (closest, window), coverage calculations (coverage, genomecov), and multi-interval analyses (multinter, intersect with multiple inputs). It can read and write common formats including BED, GFF/GTF, VCF, and BAM/SAM, and it supports format conversion and flexible output options. Outputs are typically tab-delimited and can be tailored to report overlaps, bases covered, or distinct features, making it easy to integrate into analysis pipelines.

Typical usage involves invoking bedtools with a specific command, for example bedtools <command> -a file1 -b file2, along with appropriate options (such as -wa and -wb to report the full overlapping features, or -c to count overlaps). The suite also supports multi-file operations and streaming workflows, enabling scalable analyses of large genomic datasets. It is commonly used for tasks such as annotating peaks with genes, identifying overlapping genomic features, computing coverage across regions, and summarizing interval relationships.

History and licensing: BEDTools was developed by Aaron Quinlan and colleagues and introduced in a widely cited paper describing its flexible utilities for comparing genomic features. It is released as free, open-source software under the GNU General Public License. The project is maintained as a community-driven tool with ongoing updates and expanded format support.