---
name: "bedextract"
section: "1"
platform: "linux"
package: "bedops"
version: "2.4.41+dfsg-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/bedextract"
---

# bedextract(1)

manual page for bedextract 2.4.41+dfsg

## NAME

bedextract - manual page for bedextract 2.4.41+dfsg

## DESCRIPTION

bedextract

-

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

-

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

- version:

  2\.4.41 (typical)

- authors:

  Shane Neph & Alex Reynolds

-

  Every input file must be sorted per sort-bed.

-

  USAGE:

- 0\) **--help** or **--version**

  Print requested info and exit successfully

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

  Print all unique chromosome names found in \<input.bed\>

- 2\) \<chromosome\> \<input.bed\>

  Retrieve all rows for chr8 with:  bedextract chr8 \<input.bed\>

- 3\) \<query.bed\> \<target\>

  Grab elements from the \<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). Using '-' for \<target\> indicates input (in BED format) comes from stdin.

## 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.