BEDTools statistics

Tool stats & trends

Looking to identify usage trends or leading experts?


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




No version available



  • person_outline Aaron R. Quinlan

Publication for BEDTools

BEDTools citations


Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes

Nat Commun
PMCID: 5958058
PMID: 29773832
DOI: 10.1038/s41467-018-04383-6

[…] K4me1, and H3K27ac peaks were called using the MACS2 software package at false discovery rate (FDR) ≤ 1%. SICER was used to identify enriched domains for H3K27me3 and H3K9me3. For data visualization, BEDTools in combination with in-house scripts were used to generate normalized tag density profile at a window size of 200 bp and step size of 20 bp. We also visualized the average profile around TSS […]


Methionine metabolism influences genomic architecture and gene expression through H3K4me3 peak width

Nat Commun
PMCID: 5955993
PMID: 29769529
DOI: 10.1038/s41467-018-04426-y

[…] he -broad option. Default parameters for each of these methods were used. Generation of unions and intersections of the peak sets and quantification of reads mapped to peak regions was conducted with BEDTools using the commands bedtools merge, bedtools intersect, and bedtools coverage. Extended read coverage profiles were generated using MACS2 as described previously. Raw read coverage profiles we […]


The novel 19q13 KRAB zinc finger tumour suppressor ZNF382 is frequently methylated in oesophageal squamous cell carcinoma and antagonises Wnt/β catenin signalling

PMCID: 5951945
PMID: 29760376
DOI: 10.1038/s41419-018-0604-z

[…] e. The GSM2424064_ENCFF191YCR_fold_change_over_control_GRCh38.bigWig file was downloaded. We annotated those peaks by using R package “CHIPseeker”. Subsequently, the gene region were intercepted with BEDTools and exported to Integrated Genomics Viewer software to map the peaks,. […]


Circular RNA expression and regulatory network prediction in posterior cingulate astrocytes in elderly subjects

BMC Genomics
PMCID: 5941680
PMID: 29739336
DOI: 10.1186/s12864-018-4670-5

[…] rdinates, and was therefore converted to 0-based coordinates to be consistent with the other three algorithms. We then annotated our catalog of circRNA candidates using UCSC RefSeq annotations [] and BEDtools [].The ratio of circular-to-linear RNA isoforms was calculated using the approach described in []. For each circRNA candidate, we used the number of back-spliced reads for circRNA quantificat […]


NOTCH mediated non cell autonomous regulation of chromatin structure during senescence

Nat Commun
PMCID: 5943456
PMID: 29743479
DOI: 10.1038/s41467-018-04283-9

[…] ty analysis compared to growing using the intersect of THOR and edgeR as described above. Regions displaying altered chromatin accessibility were mapped to genomic annotations or repeat regions using bedtools v2.26.0. For the genomic annotations, we used TSSs from the FANTOM database, repeats from repeatMasker (UCSC genome browser) and other genomic features (exons, introns, UTRs, etc.) were extra […]


Short genome report of cellulose producing commensal Escherichia coli 1094

Stand Genomic Sci
PMCID: 5944007
PMID: 29760866
DOI: 10.1186/s40793-018-0316-0

[…] io reads using the single-end mode of Bwa mem v0.7.4 [] with default parameters (Fig. ). Output SAM files were converted to BAM files using SAMtools v0.1.19 []. Sequencing coverage was computed using BEDtools v2.17.0 0 [] and values were normalized to 1 (genomes are haploids), from the median coverage over the large contigs (354×). The mapping coverage along the four PacBio contigs validated the s […]


Looking to check out a full list of citations?

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

star_border star_border star_border star_border star_border
star star star star star

Fabien Pichon

star_border star_border star_border star_border star_border
star star star star star
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 !