Aligning short reads to a pggb graph pangenome for SNP calling: vg map or vg giraffe

[Hanjiangna]

I have constructed a graph pangenome using pggb, and now I would like to use it as a reference to call SNPs with second-generation sequencing data. Could you kindly advise on which alignment tool would be more suitable for this purpose—vg map or vg giraffe?

Any guidance or experience sharing would be greatly appreciated. Thank you in advance!