Question about variant calling method using pangenome-graph

Question

[Marion]

Hello,

I have a question regarding the methodology for comparing the number of SNP called using giraffe on a pangenome-graph and BWA-MEM2 on a linear reference.

I read in publications two different methods.

One converts alignment in .gam to .bam using vg surject, then proceeds with a regular variant calling pipeline with the linear reference used as a backbone to construct the pangenome-graph. I saw this used in several papers, like here or here.

I also saw a second method done here where authors used vg augment from the alignments, followed by vg pack, vg snarl and finally vg call.

Is there a particular method that you would recommend for doing that?

I wish you a nice day, Regards, Marion