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