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

# starchstrip(1)

manual page for starchstrip 2.4.41+dfsg

## NAME

starchstrip - manual page for starchstrip 2.4.41+dfsg

## DESCRIPTION

starchstrip

-

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

-

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

- version:

  2\.4.41 (typical)

- authors:

  Alex Reynolds and Shane Neph

USAGE: starchstrip \[ **--include** \| **--exclude** \] \<chromosome-list\> \<starch-file\>

-

  \* Add either the **--include** or **--exclude** argument to filter the specified

-

  \<starch-file\> for chromosomes in \<chromosome-list\> for inclusion or exclusion, respectively. Note that you can only specify either inclusion or exclusion.

-

  \* The \<chromosome-list\> argument is a comma-separated list of chromosome names

-

  to be included or excluded. This list is a \*required\* argument to either of the two **--include** and **--exclude** options.

-

  \* The output is a Starch archive containing those chromosomes specified for inclusion

-

  or what chromosomes remain after exclusion from the original \<starch-file\>. A new metadata payload is appended to the output Starch archive.

-

  \* The output is written to the standard output stream **--** use the output redirection

-

  operator to write the result to a regular file, e.g.:

-

  `$ starchstrip --exclude chrA,chrB,chrC in.starch > out.starch`

-

  \* If a specified chromosome is not in the input Starch archive, it will be ignored

-

  during processing.

-

  \* Filtering simply copies over raw bytes from the input Starch archive and

-

  no extraction or recompression is performed. Use 'starchcat' to update the metadata, if new attributes are required.

-

  Process Flags **--------------------------------------------------------------------------** **--include** \<chromosome-list\>     Include specified chromosomes from \<starch-file\>.

- **--exclude** \<chromosome-list\>

  Exclude specified chromosomes from \<starch-file\>.

- **--version**

  Show binary version.

- **--help**

  Show this usage message.

## SEE ALSO

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

-

  **info starchstrip**

should give you access to the complete manual.