BEDTools specifications


Unique identifier OMICS_01159
Name BEDTools
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input format BED, BAM, VCF, GFF
Output format BED, BAM, VCF, GFF, BAI
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes


  • coverageBed
  • multiBamCov
  • mergeBed
  • IntersectBed



Add your version



  • person_outline Aaron R. Quinlan <>

BEDTools article

BEDTools citations

PMCID: 5874996

[…] of 3′ utrs with 3′ ends within 24 nt of each other to produce a non-redundant set of isoforms. all genomic interval operations were performed using pybedtools [67]. sequences were extracted using bedtools getfasta [68]., transcript-level expression of 3′ utrs was measured using sailfish v0.8.0 [28] and our curated reference library of 3′ utr sequences. to quantify the relative usage of 3′ utr […]

PMCID: 5874996

[…] ns, reads with more than 80% adenines, and reads where the last nucleotide is adenine. to annotate and quantify poly(a) sites, reads overlapping the polyasite (hg19) database were quantified using bedtools intersect (with options –s, −wa, and –c) [68], forming poly(a) site clusters. to ensure that all reads that mapped near a poly(a) site cluster were counted, we extended clusters less than 30 […]

PMCID: 5886697

[…] and the odds-ratio ≥2 (≤0.5)., adapter trimming and mapping to human and hsv-1 genomes was performed as described for the 4su-seq data. bam files with mapped reads were converted to bed format using bedtools [55] and ocrs were determined from these bed files using f-seq with default parameters [56]. no filtering of ocrs was performed. assignment of ocrs to gene promoters was performed using […]

PMCID: 5853956

[…] were visualized in the ucsc genome browser ( all libraries were normalized to the number of mapped reads per million (rpm) and bedgraph files were generated using bedtools (v2.20.1) (quinlan and hall, 2010). for log2 ratio tracks α-hp1 chip values were divided by input values and log2-transformed using bedtools (v2.20.1) (quinlan and hall, 2010). within […]

PMCID: 5821087

[…] the levenshtein distance was calculated in python using the distance module v0.1.3. analysis details can be found in jupyter notebook pst_104e_v12_post_allele_analysis submission_21092017., we used bedtools v2.25.0 (94) and the python module pybedtools (95) to perform various genome analysis tasks. this included the calculation of nearest neighbors using the closest function. details […]

BEDTools institution(s)
Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine and Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA

BEDTools review

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Fabien Pichon

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Another indispensable tools suite to have, particularly if you work with .bed files, of course !
In comparison, however, Homer is better if you want to intersect further files because it gives more details, ideal to create a Venn diagram !
A big plus of bedtools : tools are very well documented, with schemes ! I like: "shuffle" to randomly relocate peaks, to test significance of a pathway enrichment for example !