---
name: "gffutils-cli-sanitize"
section: "1"
platform: "linux"
package: "python3-gffutils"
version: "0.13-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gffutils-cli-sanitize"
---

# gffutils-cli-sanitize(1)

Sanitize a GFF file

## NAME

gffutils-cli\_sanitize - Sanitize a GFF file

## DESCRIPTION

usage: gffutils-cli sanitize \[-h\] \[--in-memory\] \[--in-place\] filename

Sanitize a GFF file. Might get merged with clean feature later.

Cleans and adds useful annotations to a GFF file:

-

  \- Ensures that start \> end in all entries - Adds an entry id (eid) to each entry to make files grep-able

Outputs result to stdout unless asked to sanitize in place.

### positional arguments:

- filename

  GFF or GTF file to use (or GFF database.)

### options:

- **-h**, **--help**

  show this help message and exit

- **--in-memory**

  Load GFF into memory for processing. (default: True)

- **--in-place**

  Sanitize file in-place: overwrites current file with sanitized version. (default: False)