---
name: "filtergtf"
section: "1"
platform: "linux"
package: "biobambam2"
version: "2.0.185+ds-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/filtergtf"
---

# filtergtf(1)

filter a gtf annotation file for use with bamfeaturecount

## NAME

filtergtf - filter a gtf annotation file for use with bamfeaturecount

## SYNOPSIS

**filtergtf \< in.gtf \> out.gtf** \[options\]

## DESCRIPTION

filtergtf filters GTF files for use with bamfeaturecount. It reads a GTF file from standard input, removes information not required by bamfeaturecount, constructs the line order as expected by bamfeaturecount (lines for a gene\_id collated, gene line first, transcript line directly before their respective exon lines) and writes the resulting GTF file to standard output.

The following key=value pairs can be given:

**T=\<filename\>:** set the prefix for temporary file names

## AUTHOR

Written by German Tischler-Höhle.

## REPORTING BUGS

Report bugs to \<germant@miltenyibiotec.de\>

## COPYRIGHT

Copyright © 2009-2019 German Tischler-Höhle, © 2011-2014 Genome Research Limited. License GPLv3+: GNU GPL version 3 \<http://gnu.org/licenses/gpl.html\>\
 This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law.