BEDEXTRACT(1)

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

💖 NAME 💖

bedextract — bestie, it's the manual page for bedextract 2.4.42+dfsg, and she's serving 🫶

✨ DESCRIPTION ✨

Okay so, <pink>bedextract</pink> is the tool, and here's the whole vibe check on her 💅

citation: 🎀

version: 2.4.42 (typical)

authors: Shane Neph & Alex Reynolds 👑

Heads up, bestie: every input file must be sorted per sort-bed. Not optional. No cap. 🙈

🌸 USAGE 🌸

0) --help or --version

Prints the info you asked for and exits successfully. She ate and left no crumbs ✨

1) --list-chr <input.bed>

Prints all unique chromosome names found in <input.bed>. It's giving chromosome inventory 🦋

2) <chromosome> <input.bed>

Retrieve all rows for chr8 with:

bedextract chr8 <input.bed>

Iconic. Literally just grab a whole chromosome's worth of rows. 💜

3) <query.bed> <target>

Grab elements from <query.bed> that overlap elements in <target>. Same as

bedops -e 1 <query.bed> <target>

…except that this option fails silently if <query.bed> contains fully-nested BED elements. 💀

If no fully-nested element exists, bedextract can vastly improve upon the performance of bedops. 🔥

<target> may be a BED or Starch file (with or without fully-nested elements). And using - for <target> means the input (in BED format) comes from stdin. Main character stdin energy 👑

👑 SEE ALSO 👑

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

info bedextract

should give you access to the complete manual. Go read her, bestie, iykyk 📖✨

That's a wrap, gorgeous 💖 This was bedextract 2.4.42+dfsg, from August 2025, filed under BEDEXTRACT(1). Slay, periodt. 🎀🦋💅

📦 where this page comes from