Extract alignment between two samples from a GFA?

Question

[cmdcolin]

Hi all

I am trying to learn about graph genomes, and was wondering if there was a way to "extract a pairwise alignment" between two samples

I am looking at the HPRC data as an example https://github.com/human-pangenomics/hpp_pangenome_resources

It looks like the minigraph-cactus GFA has "walks" for each sample (which I think is required for this exercise, the minigraph-only has just S and L lines while the minigraph-cactus has S, L, and W lines...with the W lines encoding sample specific walk paths (i think?))

Some possible approaches I thought of were:

• rgfa2paf but not sure if HPRC data is rGFA
• somehow converting to HAL, and then extracting MAF, and then converting MAF to PAF for the samples I'm interested in (?) https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/progressive.md#maf-export

but, I'm also not familiar with a lot of tools out there, so if something already exists or is closer to this goal, let me know!