BEDOPS pipeline

BEDOPS specifications


Unique identifier OMICS_00949
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Input data BEDOPS supports a relaxed variation of the BED specification, to which several popular formats, including WIG, SAM/BAM, VCF and GFF, readily convert. Thus, data currently stored in any of these formats can be transformed and analyzed using features offered by BEDOPS.
Input format BED, WIG, SAM, BAM, VCF, GFF,
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.4.15
Stability Stable
Maintained Yes



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Publication for BEDOPS

BEDOPS citations

PMCID: 5506536

[…] output written to / dev/null. valr functions performed similarly or faster than bedtools commands, with the exception of bed_map and bed_fisher ( figure 3b)., command-line tools like bedtools and bedops can be incorporated into reproducible workflows (e.g., with snakemake 11), but it is cumbersome to transition from command-line tools to exploratory analysis and plotting software. rmarkdown […]

PMCID: 4049842

[…] of all the commands used, are available at, figure 1 was generated using the cytoscape software [34]. to manipulate genome-wide data, we used the bedops [35] and the bedtools [36] suites., we would like to thank joshua payne, kathleen sprouffske, josé aguilar-rodríguez, and the members of the andreas wagner group in zurich for useful feedback […]

BEDOPS institution(s)
Department of Genome Sciences, University of Washington, Seattle, WA, DC, USA; Department of Medicine, University of Washington, Seattle, WA, DC, USA
BEDOPS funding source(s)
National Institutes of Health Grants (1U54HG004592 and 5U01ES017156)

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