BEDOPS(1)

📦
version 2.4.42 · 5 versions
, in ubuntu resolute, ubuntu stonking

✨ NAME ✨

okay so this is the manual page for bedops — that's the bedops from version 2.4.42+dfsg, bestie 💖

🦋 DESCRIPTION 🦋

bedops 💅 the way that this little icon does so much...

citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract

https://doi.org/10.1093/bioinformatics/bts277

version: 2.4.42 (typical)

authors: Shane Neph & Scott Kuehn 👑

Here's the whole vibe of how you call it:

USAGE: bedops [process-flags] <operation> <File(s)>*

okay ground rules, no cap 📋

  • Every single input file has to be sorted per the sort-bed utility. literally non-negotiable. and each operation needs a minimum number of files, which is shown down below in the operations list.
  • There is no fixed maximum number of files you can throw at it. go off, pile them on 🌈
  • Input files must have at least the first 3 columns of the BED specification. The program accepts BED and Starch file formats.
  • You may use - for a file to mean "read from standard input" — but that's BED format only, okurrr? ✨

🎀 Process Flags 🎀

  • --chrom <chromosome> — jump to and process data for that <chromosome> only. just that one. tunnel vision, main character energy 💅
  • --ec — error check input files. yes it's slower. yes it's worth it 🫶
  • --header — accept headers (VCF, GFF, SAM, BED, WIG) in any input file. let them in, bestie 🙈
  • --help — print this message and exit successfully. slay ✨
  • --help-<operation> — detailed help on <operation>. An example is --help-c or --help-complement
  • --range L:R — add L bp to all start coordinates and R bp to end coordinates. Either value may be + or - to grow or shrink regions. With the -e/-n operations, the first (reference) file is not padded, unlike all other files. ⚠️
  • --range S — pad or shrink input file(s) coordinates symmetrically by S. This is shorthand for: --range -S:S.
  • --version — print program information.

🌈 Operations 🌈 (choose one of)

  • -c, --complement [-L] File1 [File]*
  • -d, --difference ReferenceFile File2 [File]*
  • -e, --element-of [bp | percentage] ReferenceFile File2 [File]*

by default, -e 100% is used. bedops -e 1 is also popular.

  • -i, --intersect File1 File2 [File]*
  • -m, --merge File1 [File]*
  • -n, --not-element-of [bp | percentage] ReferenceFile File2 [File]*

by default, -n 100% is used. bedops -n 1 is also popular.

  • -p, --partition File1 [File]*
  • -s, --symmdiff File1 File2 [File]*
  • -u, --everything File1 [File]*
  • -w, --chop [bp] [--stagger <nt>] [-x] File1 [File]*

by default, -w 1 is used with no staggering.

💜 Example 💜

bedops --range 10 -u file1.bed
NOTE: Only operations -e|n|u preserve all columns (no flattening). the others will flatten on you, iykyk 😭

🌸 SEE ALSO 🌸

The full documentation for bedops is maintained as a Texinfo manual. If the info and bedops programs are properly installed at your site, the command

info bedops

should give you access to the complete manual. go read it, it's giving lore 📖✨

and that's a wrap, bestie 🎀 this was bedops 2.4.42+dfsg, dropped in August 2025, living its truth as BEDOPS(1). periodt. 💅💖

📦 where this page comes from