agat_sp_fix_overlaping_genes.pl

DESCRIPTION

Check a gtf/gff annotation file to find cases where differents gene features have CDS that overlap. In this case the gene features will be merged in only one. One gene is choosen 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.

• -o, --out, --output or --outfile

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

• --help or -h

  Display this helpful text.