Add a shared locus tag per record. A record is all features linked by each other by parent/children relationship (e.g Gene,mRNA,exon, CDS).

SYNOPSIS --gff <input file> [-o <output file>] --help


  • --gff, --file or --input

    STRING: Input GTF/GFF file.

  • -p, --type or -l

    Primary tag option, case insensitive, list. Allow to specied the Level1 feature types that will be handled. By default all feature Level1 are taken into account.

  • --lo or --to

    Locus tag output, by defaut it will be called locus_tag, but using this option you can specied the name of this attribute.

  • --li or --ti

    Tag input, by default the value of the locus tag attribute will be locusX where X is an incremented number. You can use the values of an existing attribute instead e.g the ID value: --li ID.

  • --of

    Output format, if no ouput format is given, the same as the input one detected will be used. Otherwise you can force to have a gff version 1 or 2 or 3 by giving the corresponding number.

  • -o or --output

    STRING: Output file. If no output file is specified, the output will be written to STDOUT. The result is in tabulate format.

  • -q or --quiet

    To remove verbosity.

  • -c or --config

    String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).

  • --help or -h

    Display this helpful text.