compare vg stat scores

Question

[aaaniich]

Hey, everybody! I'm trying to decide between two pangenomes. I have called short reads and got vg stat for two of them. I can see that the scores are higher for the second one. But I'm wondering how much they are vg stats and is it bad that softclips are also higher in the second one?

[Jordan M Eizenga]

I don't think it's a total slam dunk for either one. It looks to me like pangenome 1 is getting somewhat better base-level alignments, but pangenome 2 is noticeably faster. In any case, the difference in alignment accuracy is small (mostly at the 3rd digit), so either one will probably work fine.