BEDTools pipeline

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
  • IntersectBed
  • mergeBed
  • multiBamCov



Add your version



  • person_outline Aaron R. Quinlan <>

Publication for BEDTools

BEDTools IN pipelines

PMCID: 5760651
PMID: 29317678
DOI: 10.1038/s41467-017-02618-6

[…] orientation were collapsed to a single read before subsequent analysis. density profiles were created by extending each read to the average library fragment size and then computing density using the bedtools suite. enriched regions were discovered using macs 2.0 and scored against matched input libraries. genomic ‘blacklisted’ regions were filtered […]

PMCID: 5770421
PMID: 29339748
DOI: 10.1038/s41467-017-02759-8

[…] mutant and wild-type cells were calculated using bamcompare in the deeptools, a data analysis program for high-throughput sequencing. the read counts and rpkm values were identified using the bedtools and bwtool utility program. rpkm values were calculated as: rpkm = (number of reads mapped to a gene × 1e + 09)/ (length of the gene × number of total mapped read counts in the experiment). […]

PMCID: 5773227
PMID: 29346435
DOI: 10.1371/journal.ppat.1006796

[…] -m, converts the output to bam using picard sortsam (v. 1.130;, and retains only the reads that have the most common mapped start and stop coordinates using bedtools (v. 2.19.1)[48]. reads were collapsed into consensus sequences using with options—ambig 600—min_freq 0.75 to require that the consensus base called makes […]

PMCID: 5775534
PMID: 29351814
DOI: 10.1186/s13059-017-1376-y

[…] peak detection using macs2. to identify repeats enriched for h4r3me2s, the number of chip-seq peaks overlapping each repeat class were compared with a random control where peaks were shuffled (using bedtools) over mappable regions of the genome. rna-seq data were aligned to mm9 using tophat v2.0.9 [45] with -g 1 option, which assigns reads with multiple hits of equal quality to one […]

PMCID: 5780849
PMID: 29363428
DOI: 10.1186/s12864-017-4374-2

[…] around a-to-i rna editing sites in human and mouse was delineated in two steps: 1) extracting the profile of up- and down-stream sequences (15 bases on each side) flanking editing sites using bedtools getfasta [53]; 2) visualizing the sequence context around rna editing sites using weblogo 3(weblogo –a dna –c classic –units probability –first-index −10) [54]., level of expressed genes […]

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 !