---
name: "flattenGTF"
section: "1"
platform: "linux"
package: "subread"
version: "2.0.8+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/flattenGTF"
---

# flattenGTF(1)

toolkit for processing next-gen sequencing data

## NAME

flattenGTF - toolkit for processing next-gen sequencing data

## DESCRIPTION

flattenGTF Version 2.0.4

-

  Flatten features included in a GTF annotation and save the modified annotation to a SAF format file.

### Usage:

-

  ./flattenGTF \[options\] **-a** \<input\_file\> **-o** \<output\_file\>

\## Mandatory arguments:

- **-a** \<file\>

  Name of an annotation file in GTF/GFF format.

- **-o** \<file\>

  Name of output file.

\## Optional arguments:

- **-t** \<string\>

  Specify feature type in a GTF annotation. 'exon' by default. Features with the specified feature type are extracted from the annotation for processing.

- **-g** \<string\>

  Specify attribute type in GTF annotation. 'gene\_id' by default. This attribute type is used to group features into metafeatures.

- **-C**

  Merging overlapping exons into multiple non-overlapping exons but all the edges are kept.

## AUTHOR

 This manpage was written by Alexandre Mestiashvili for the Debian distribution and\
  can be used for any other usage of the program.