BEDOPS protocols

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 IN pipelines

PMCID: 5457497
PMID: 28534499
DOI: 10.1038/ncomms15264

[…] reads sharing the same fusion point within a 5nt window were clustered. fusions were classified as genic/intergenic and concordant/discordant using a combination of bedtools 2.16.2 (ref. 62) and bedops 2.30 (ref. 63). htlv-1/blv integration sites were determined based on identification of chimeric transcripts that encompassed ltr-host boundaries. hybrid reads generated from 3′as-enriched […]

PMCID: 4707743
PMID: 26702038
DOI: 10.1098/rspb.2015.1746

[…] genes across a range of developmental stages were calculated with use of the rsem package [31] as described previously [20]. the neighbouring pairs were identified using closest-features in the bedops toolkit v. 2.4.3 [32]. the spearman correlation between pairs of a lincrna and its neighbour gene was calculated in r v.3.1.2 [33], and p-values were corrected for multiple comparisons […]

PMCID: 4049842
PMID: 24911413
DOI: 10.1371/journal.pone.0099424

[…] 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 […]

PMCID: 4254438
PMID: 25473426
DOI: 10.1186/s13073-014-0087-1

[…] querying for variants by database identifiers (such as dbsnp or refsnp ids) or by genomic position. for larger analyses, automated approaches are clearly required. toolkits such as bedtools [12] and bedops [13] implement efficient data structures and algorithms to carry out these analyses on a genome scale very quickly. both packages take as input databases of genomic elements in standard file […]

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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