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pybedtools specifications


Unique identifier OMICS_09508
Name pybedtools
Software type Package/Module
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 Python
License GNU General Public License version 2.0
Computer skills Advanced
Version 0.6.9
Stability Stable
Maintained Yes




No version available



  • person_outline Aaron R. Quinlan

Publication for pybedtools

pybedtools citations


Global profiling of protein–DNA and protein–nucleosome binding affinities using quantitative mass spectrometry

Nat Commun
PMCID: 5916898
PMID: 29695722
DOI: 10.1038/s41467-018-04084-0

[…] 38 using the UCSC genome browser liftOver tool. All G4 peaks from the plus and minus strand with overlapping coordinates were combined using bedtools. We used automated permutation-based testing with pybedtools to look for significant correlation between ChIP-seq peaks and G4-seq peaks. We randomized ChIP-seq peaks 1000 times over the genome and each time measured the peak intersection with G4-seq […]


Bamgineer: Introduction of simulated allele specific copy number variants into exome and targeted sequence data sets

PLoS Comput Biol
PMCID: 5891060
PMID: 29590101
DOI: 10.1371/journal.pcbi.1006080

[…] Bamgineer uses several python packages for parsing input files (pyVCF[], VCFtools[], and pybedtools[], manipulating BAM files (pysam[], Samtools[], Sambamba[] and BamUtils[]), phasing haplotypes (BEAGLE[], and distributing compute jobs in cluster environments (ruffus[]). HaplotypeCaller f […]


uvCLAP is a fast and non radioactive method to identify in vivo targets of RNA binding proteins

Nat Commun
PMCID: 5861125
PMID: 29559621
DOI: 10.1038/s41467-018-03575-4

[…] k centers were used. Motifs were generated based on the 5% highest-scoring peaks among the 10,000 bound training instances.Venn diagrams comparing uvCLAP, PAR-CLIP, and eCLIP peaks were created using pybedtools (version 0.7.9). […]


Argonaute2 and LaminB modulate gene expression by controlling chromatin topology

PLoS Genet
PMCID: 5864089
PMID: 29529026
DOI: 10.1371/journal.pgen.1007276

[…] We therefore selected final peaks for Pol II as those peaks in the pooled peak-calling run that were also found in at least one of the individual replicates. Specifically, using BEDTools v2.25.0 and pybedtools v0.7.9 [,] we used "pooled.intersect([replicates], u = True).sort().merge()" where "pooled" points to the pooled peak calls and "[replicates]" is the list of individual peak calls for each […]


A Near Complete Haplotype Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici Reveals High Interhaplotype Diversity

PMCID: 5821087
PMID: 29463659
DOI: 10.1128/mBio.02275-17

[…] github information.We also performed a detailed coverage sequence depth analysis on 1-kb sliding windows by using 200-base intervals. We generated corresponding bed files with the window function in pybedtools for primary contigs and haplotigs. In addition, we generated corresponding sliding window bed files for primary contig regions that aligned with haplotig regions and for regions that lacked […]


Integration of Kinase and Calcium Signaling at the Level of Chromatin Underlies Inducible Gene Activation in T Cells

PMCID: 5632840
PMID: 28904128
DOI: 10.4049/jimmunol.1602033

[…] For ATAC-seq, Venn diagrams were obtained using pybedtools (). For RNA-seq, BioVenn was used (). […]


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pybedtools institution(s)
Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA; Department of Medicine, University of Colorado, Denver, Anschutz Medical Campus, Aurora, CO, USA; Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
pybedtools funding source(s)
Intramural Program of the National Institute of Diabetes and Digestive and Kidney Diseases

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