This script is a kind of annotation filter by sequence name. It goes through the gff annotation features and remove those that are not linked to a sequence from the fasta file provided. The match between sequence name in the fasta file and the 1st column of the gff3 file is case sensitive.

SYNOPSIS --gff <gff_file.gff> --fasta <fasta_file.fa> [-o <output file>] --help


  • --gff, --file or --input

    STRING: Input GTF/GFF file.

  • -f or --fasta

    STRING: fasta file.

  • -v or --verbose

    For verbosity

  • -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.