-a option can now be used with
vg call to add reference calls: https://github.com/vgteam/vg/pull/2966
vg call -a ... -s sample1 > sample1.vcf vg call -a ... -s sample2 > sample2.vcf
bcftools merge sample1.vcf.gz sample2.vcf.gz -m all to make the combined VCF.
This only works right now in "genotyping mode", where you construct a graph from a VCF with
vg construct -a then genotype that same VCF with
vg call -v.
I'm hoping to have a solution for general graphs, in the form of an option that makes
vg call call every site with consistent positions no matter what, within the next week or so. It's coming up as a problem for many people.