This script fixes and/or standardizes any GTF/GFF file into full sorted GTF/GFF file. It AGAT parser removes duplicate features, fixes duplicated IDs, adds missing ID and/or Parent attributes, deflates factorized attributes (attributes with several parents are duplicated with uniq ID), add missing features when possible (e.g. add exon if only CDS described, add UTR if CDS and exon described), fix feature locations (e.g. check exon is embedded in the parent features mRNA, gene), etc...

All AGAT's scripts with the sp prefix use the AGAT parser, before to perform any supplementary task. So, it is not necessary to run this script prior the use of any other sp script.

SYNOPSIS -g infile.gff [ -o outfile ] --help


  • -g, --gff or -ref

    String - Input GTF/GFF file. Compressed file with .gz extension is accepted.

  • -v

    Integer - Verbose option. To modify verbosity. Default is 1. 0 is quiet, 2 and 3 are increasing verbosity.

  • -o or --output

    String - Output GFF file. If no output file is specified, the output will be written to STDOUT.

  • -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).

  • -h or --help

    Boolean - Display this helpful text.