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

# gffutils-cli(1)

Command line interface for python-gffutils.

## NAME

gffutils-cli - Command line interface for python-gffutils.

## DESCRIPTION

usage: gffutils-cli \[-h\]

-

  {fetch,children,parents,region,create,common,clean,search,sanitize,rmdups} ...

### positional arguments:

-

  {fetch,children,parents,region,create,common,clean,search,sanitize,rmdups}

- fetch

  Fetch IDs.

- children

  Fetch children from the database according to ID.

- parents

  Fetch parents from the database according to ID.

- region

  Returns features within provided genomic coordinates.

- create

  Create a database.

- common

  Identify child features in common (e.g., common exons across multiple isoforms)

- clean

  Perform various QC operations to clean a GFF or GTF file.

- search

  Search the attributes.

- sanitize

  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.

- rmdups

  Remove duplicates from a GFF file.

### options:

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

  show this help message and exit