Recommended practices for downstream analyses

[agolicz]

Hello,
I was wondering are there recommended practices for downstream analyses with pggb graphs? We are especially interested in variant genotyping from short reads for GWAS and transcript expression quantification from short reads for eQTL. rpvg seems really helpful for plant eQTL analysis but we only tried it with vg built graphs so far.
All the best,
Agnieszka