About: Bedops

The utilities in the BEDOPS software suite help to address common questions raised during genomics studies, mostly with regard to overlap and proximity relationships between data sets. A prominent advantage of the utilities over related software is scalability: the tools are designed to work with arbitrarily large data in a relaxed BED format.

You can download code and binaries at the bedops GitHub site. You can also discuss the BEDOPS suite at our users forum.

The utilities in the suite are:

bedmap
takes a reference file and a mapping file and calculates, per reference file entry, summary statistics using overlapping elements from the mapping file.
bedops
offers several set and multiset operations, including union, subset, and difference, to assist investigators with finding relationships between two or more genomic datasets
closest-features
associates features between two inputs based upon genomic distance measures.
sort-bed
sorts a BED file defined first by lexicographic chromosome order, then ascending integer start coordinate order, and finally by ascending integer end coordinate order.
starch and unstarch
efficient compression and extraction of BED-formatted data.
convert2bed
The convert2bed binary converts common binary and text genomic formats (BAM, GFF, GTF, GVF, PSL, RepeatMasker annotation output (OUT), SAM, VCF and WIG) to unsorted or sorted, extended BED or BEDOPS Starch (compressed BED) with additional per-format options. Convenience wrapper bash scripts are provided for each of these input formats, as well as script variants for parallelization of conversion work with SGE and GNU Parallel environments.
bedextract
efficient data extraction from BED-formatted data.