The script aims to add splice sites features (five_prime_cis_splice_site and three_prime_cis_splice_site) to gtf/gff file. The splice sites are deduced from CDS features.

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


  • --gff, -f, --ref or -reffile

    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).

  • --help or -h

    Display this helpful text.