The script aims to compute the Sensitivity and Specificity in order to assess the quality of an annotation according to a reference (that is supposed to be true high-quality annotation). The Sensitivity (Sn) is the proportion of true predictions compared to the total number of correct genes (including missed predictions) Sn = TP / TP+FN The Specificity (Sp) is the proportion of true predictions among all predicted genes (including incorrectly predicted ones) Sp = TP / TP+FP

reference annotation: ------------- prediction : ------------ FN TP FP TN

Sensitivity and Specificity will be computed for each feature types. (and computed independentaly if part of different Level2 type. i.e. exons Sn Sp for tRNA will not be mixed up with the exon Sn Sp of mRNA exons)

SYNOPSIS --gff1 infile1.gff --gff2 infile2.gff  [ -o outfile ] --help


  • -gff1

    Input GTF/GFF file 1.

  • -gff2

    Input GTF/GFF file 2.

  • -o , --output , --out or --outfile

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

  • -v

    Verbose option for debug purposes.

  • -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

    Display this helpful text.