The script aims to remove incomplete gene models. An incomplete gene coding model is a gene coding with start and/or stop codon missing in its cds. You can modify the behavior using the skip_start_check or skip_stop_check options.

SYNOPSIS --gff infile.gff --fasta genome.fa [ -o outfile ] --help


  • -gff

    Input GTF/GFF file.

  • -fa or --fasta

    Genome fasta file. The name of the fasta file containing the genome to work with.

  • --ct or --table or --codon

    This option allows specifying the codon table to use. It expects an integer [default 1]

  • --ad or --add_flag

    Instead of filter the result into two output files, write only one and add the flag <incomplete> in the gff.(tag = inclomplete, value = 1, 2, 3. 1=start missing; 2=stop missing; 3=both)

  • --skip_start_check or --sstartc

    Gene model must have a start codon. Activated by default.

  • --skip_stop_check or --sstopc

    Gene model must have a stop codon. Activated by default.

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

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

  • -v

    Verbose option, make it easier to follow what is going on for debugging purpose.

  • -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.