GT-EVAL(1)

NAME
gt-eval - Compare annotation files and show accuracy measures (prediction vs. reference).

SYNOPSIS

gt eval reference_file prediction_file

OPTIONS

-nuc
    evaluate nucleotide level (memory consumption is proportional to the input file sizes) (default: yes)

-ltr
    evaluate a LTR retrotransposon prediction instead of a gene prediction (all LTR_retrotransposon elements are considered to have an undetermined strand) (default: no)

-ltrdelta
    set allowed delta for LTR borders to be considered equal (default: 20)

-v
    be verbose (default: no)

-o
    redirect output to specified file (default: undefined)

-gzip
    write gzip compressed output file (default: no)

-bzip2
    write bzip2 compressed output file (default: no)

-force
    force writing to output file (default: no)

-help
    display help and exit

-version
    display version information and exit

DESCRIPTION

The program shows sensitivity and specificity values for certain feature types (e.g., gene, mRNA, and exon). For some feature types the number of missing and wrong features of that type is also shown. Thereby, “missing” means the numbe r of features of that type from the “reference” without overlap to a feature of that type from the “prediction”. Vice versa, “wrong” denotes the number of features of that type from the “prediction” without overlap to a feature of that type from the “reference”.

AUTHOR

Report bugs to <gt-users@genometools.org>.