vg call -v from autoindex

[BaxW]

Say I have a phased VCF of variants called vars.vcf I want to genotype in a broader set of samples, so I use it to index and map like this:

vg autoindex --workflow giraffe -r  ref.fa -v vars.vcf
vg giraffe  -Z graph.giraffe.gbz -m graph.shortread.withzip.min -d graph.dist -f reads1.fa -f reads2.fa  > sample.giraffe.gam

then I call like this:

 vg pack -x graph.giraffe.gbz -g sample.giraffe.gam -o sample.pack
 vg snarls  graph.giraffe.gbz > graph.snarls
 vg call graph.giraffe.gbz -z -a -k sample.pack -r graph.snarls  > sample.vcf

I want the alleles/variants in sample.vcf to be directly comparable to those in the the original (vars.vcf) I understand that using vg call -z is supposed to limit possible alleles to those in represented in the haplotypes of the .gbz, which is why I use it... However, I read here that sample.vcf would have some variants represented differently than the original vars.vcf.

For the vcf output by vg call to have the exact same representation of variants as the original VCF, I could use vg call --vcf vars.vcf. But in order to do that, I would have to construct the graph with vg construct -a vars.vcf and then manually make the indexes for giraffe, correct?

Is there any way to use vg call -v in this context without reconstructing and re-indexing the graph? Is it possible to use vg call with both-v and -z?

Thanks!