The script changes IDs to give uniq one and reflect the change in Parent attribute of impacted features.

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


  • --gff, --file or --input

    STRING: Input GTF/GFF file.

  • --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.

  • -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.