I’m planning to construct a pangenome for different varieties of the same species, where each variety has a corresponding genome file and GFF file. My approach is to build a pangenome for each chromosome using PGGB or Minigraph-Cactus and then merge these to get the final pangenome. I have two questions:

Since vg rna only accepts one pangenome and one GFF file, I’m not sure how to handle the GFF files. Should I standardize the gene names across different varieties and merge all the GFF files together?

If there’s only one GFF file, how can I distinguish between transcripts that are haplotype-specific (variety-specific)?

Thanks for your help.