The script aims to add intergenic features (intergenic_region) to gtf/gff file. The intergenic regions are deduced from gene features (feature type gene from the 3rd column).

SYNOPSIS --gff infile --out outFile --help


  • --gff, -f or --ref

    Input GTF/GFF file.

  • --out, --output or -o

    Output file (default GFF3 - see config to modify output 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 yo the possibility to use your own AGAT config file (located elsewhere or named differently).

  • -v or --verbose

    Add verbosity

  • -h or --help

    Display this helpful text.