This script merge different gff annotation files in one. It uses the AGAT parser that takes care of duplicated names and fixes other oddities met in those files.

SYNOPSIS --gff infile1 --gff infile2 --out outFile --help


  • --gff or -f

    Input GTF/GFF file(s). You can specify as much file you want like so: -f file1 -f file2 -f file3

  • --out, --output or -o

    Output gff3 file where the gene incriminated will be write.

  • -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.