The script aims to list all the introns inferior to a certain size. Introns are calculated on the fly from exons. (intron feature will not be used).

SYNOPSIS --gff infile [ --out outFile ] --help


  • --gff, -f, --ref or -reffile

    Input GTF/GFF file.

  • --size or -s

    Minimum intron size accepted in nucleotide. All introns under this size will be reported. Default value = 10.

  • --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.