agat_sp_fix_overlaping_genes.pl

DESCRIPTION

Check a GTF/GFF annotation file to find cases where different gene features have CDS that overlap. In this case the gene features will be merged in only one. One gene is chosen as reference, and the mRNA from the other gene will be linked to it. So, it creates isoforms.

SYNOPSIS

agat_sp_fix_overlaping_genes.pl -f infile  [-o outfile]
agat_sp_fix_overlaping_genes.pl --help

OPTIONS

  • -f, --file, --gff3 or --gff

    Input GTF/GFF file.

  • -m or --merge

    Bolean: Merge/add the attributes of gene feature that are merged (except ID and Parent).

  • -o, --out, --output or --outfile

    Output file. If none given, will be display in standard output.

  • -v or --verbose

    BOLEAN: Add verbosity.

  • --help or -h

    Display this helpful text.