BEDTools

Application data
Created by	Aaron Quinlan
Biological application domain(s)	Genomics
Principal bioinformatics method(s)	Mapping
Created at	University of Virginia
Maintained?	Yes
Input format(s)	BED, BAM, GFF
Output format(s)	BED, BAM, GFF
Software features	Feature overlaps, UNIX pipes, coverage, BAM support
Programming language(s)	C++
Licence	GPLv2
Operating system(s)	UNIX/Linux, MacOS X

Summary: BEDTools is an extensive suite of utilities for comparing genomic features in BED format.

"Error: no local variable "counter" was set." is not a number.

The BEDTools utilities allow one to address common genomics tasks such finding feature overlaps and computing coverage. In addition, one can develop sophisticated pipelines that answer complicated research questions by "streaming" several BEDTools together. The following are examples of common questions that one can address with BEDTools.

Intersecting two BED files in search of overlapping features. Merging overlapping features. Screening for paired-end (PE) overlaps between PE sequences and existing genomic features. Calculating the depth and breadth of sequence coverage across defined "windows" in a genome. The fact that all of the BEDTools accept input from “stdin” allows one to “stream / pipe” several commands together to facilitate more complicated analyses. Also, the tools allow fine control over how output is reported. Most recently, we have added support for sequence alignments in BAM (http://samtools.sourceforge.net/) format, as well as for features in GFF and “blocked” BED format. The tools are quite fast and typically finish in a matter of a few seconds, even for large datasets.