This script takes a normal gff3 annotation format file and convert it to gff3 like ensembl format.

SYNOPSIS -g infile.gff [ -o outfile ] --help


  • -g, --gff or -ref

    Input GTF/GFF file.

  • -c or --ct

    When the gff file provided is not correcly formated and features are linked to each other by a comon tag (by default locus_tag), this tag can be provided to parse the input file correctly.

  • -v

    Verbose option to see the warning messages when parsing the gff file.

  • -o or --output

    Output GFF file. If no output file is specified, the output will be written to STDOUT.

  • -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).

  • -h or --help

    Display this helpful text.