i am not sure how about the data input format but 'hisat2' is able to 'align rna-seq to a population reference'. this may be a little different than aligning directly to the human pangenome graph, but may be a point of reference. can also come up with various links by searching the vg repository, one link i found here https://github.com/vgteam/vg/wiki/Transcriptomic-analyses I have not done a lot of work with graph genomes but i'd say that it is likely a challenging endeavor compared with reference based, but could be interesting :)

The vg mpmap subcommand has features for mapping RNA-seq data to a graph. We describe in more detail in this publication, including a comparison to some other tools you might consider. cmdcolin is correct that HISAT2 is also capable of aligning to a graph that is constructed from a VCF.

If you plan to use VCF data, minigraph isn't really an appropriate tool. It's designed for building a graph from multiple genome assemblies. For VCF input, HISAT2 and vg both have internal graph construction algorithms. I can't speak much for HISAT2, but the easiest entry point for vg's graph construction (for most people) is the vg autoindex subcommand.