---
name: "gt-gff3"
section: "1"
platform: "linux"
package: "genometools"
version: "1.6.5+ds-2.2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gt-gff3"
---

# gt-gff3(1)

Parse, possibly transform, and output GFF3 files.

## NAME

gt-gff3 - Parse, possibly transform, and output GFF3 files.

## SYNOPSIS

**gt gff3** \[option ...\] \[GFF3\_file ...\]

## DESCRIPTION

- **-sort** \[*yes\|no*\]

  sort the GFF3 features (memory consumption is proportional to the input file size(s)) (default: no)

- **-sortlines** \[*yes\|no*\]

  sort the GFF3 features on a strict line basis (not sorted asdefined by GenomeTools) (default: no)

- **-sortnum** \[*yes\|no*\]

  enable natural numeric sorting for sequence regions (not sorted as defined by GenomeTools) (default: no)

- **-tidy** \[*yes\|no*\]

  try to tidy the GFF3 files up during parsing (default: no)

- **-retainids** \[*yes\|no*\]

  when available, use the original IDs provided in the source file (memory consumption is proportional to the input file size(s)) (default: no)

- **-checkids** \[*yes\|no*\]

  make sure the ID attributes are unique within the scope of each GFF3\_file, as required by GFF3 specification (memory consumption is proportional to the input file size(s)). If features with the same Parent attribute are not separated by a *#* line the GFF3 parser tries to treat them as a multi-line feature. This requires at least matching sequence IDs and types. (default: no)

- **-addids** \[*yes\|no*\]

  add missing "##sequence-region" lines automatically (default: yes)

- **-fixregionboundaries** \[*yes\|no*\]

  automatically adjust "##sequence-region" lines to contain all their features (memory consumption is proportional to the input file size(s)) (default: no)

- **-addintrons** \[*yes\|no*\]

  add intron features between existing exon features (default: no)

- **-offset** \[*value*\]

  transform all features by the given offset

- **-offsetfile** \[*filename*\]

  transform all features by the offsets given in file (default: undefined)

- **-setsource** \[*string*\]

  set the *source* value (2nd column) of each feature (default: undefined)

- **-typecheck** \[*string*\]

  use an ontology given in an OBO file to validate parent-child relationships. If no argument is given, the sofa.obo file from the gtdata/obo\_files directory is used. If an argument is given, it is used as an OBO filename. In the case that such a file does not exist *.obo* is added to the argument and loading the resulting filename from the gtdata/obo\_files directory is attempted. (default: undefined)

- **-xrfcheck** \[*string*\]

  check Dbxref and Ontology\_term attributes for correct syntax according to a abbreviation definition file. If no argument is given, the GO.xrf\_abbs file from the gtdata/xrf\_abbr directory is used. If an argument is given, it is used as an specific filename for an abbreviation file. In the case that such a file does not exist, *.xrf\_abbr* is added to the argument and loading the resulting filename from the gtdata/xrf\_abbr directory is attempted. (default: undefined)

- **-show** \[*yes\|no*\]

  show GFF3 output (default: yes)

- **-v** \[*yes\|no*\]

  be verbose (default: no)

- **-width** \[*value*\]

  set output width for FASTA sequence printing (0 disables formatting) (default: 0)

- **-o** \[*filename*\]

  redirect output to specified file (default: undefined)

- **-gzip** \[*yes\|no*\]

  write gzip compressed output file (default: no)

- **-bzip2** \[*yes\|no*\]

  write bzip2 compressed output file (default: no)

- **-force** \[*yes\|no*\]

  force writing to output file (default: no)

- **-help**

  display help and exit

- **-version**

  display version information and exit

File format for option *-offsetfile*:

The file supplied to option *-offsetfile* defines a mapping table named “offsets”. It maps the sequence-region entries given in the GFF3\_file to offsets. It can be defined as follows:

```
offsets = {
  chr1  = 1000,
  chr2  = 500
}
```

When this example is used, all features with seqid “chr1” will be offset by 1000 and all features with seqid “chr2” by 500.

If *-offsetfile* is used, offsets for all sequence-regions contained in the given GFF3 files must be defined.

## REPORTING BUGS

Report bugs to https://github.com/genometools/genometools/issues.