The script reads a gff annotation file, and create two output files, one contains the gene models with ORF passing the test, the other contains the rest. By default the test is "> 100" that means all gene models that have ORF longer than 100 Amino acids, will pass the test.

SYNOPSIS --gff infile.gff [ -o outfile ] -h


  • -g or --gff

    Input GTF/GFF file.

  • -s or --size

    ORF size to apply the test. Default 100.

  • -t or --test Test to apply (> < = >= <=). If you us one of these two character >, <, please don't forget to quote you parameter liket that "<=". Else your terminal will complain. By default it will be ">"

  • -v

    Verbose. Useful for debugging purpose. Bolean

  • -o or --out or --output or --outfile

    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.