How to obtain the nodes in the graph corresponding to the variant in VCF

Question

[Wenhai]

I constructed a variation graph with a vcf file and a reference genome using vg construct. I hope to obtain the nodes in the graph corresponding to the variant in VCF. But I don't find the easy way to get it, although I believe that information can be obtained by traversing the reference path and connecting edges. Could you please help me? Thanks.

Answer 1

[agis.maulana12]

Straightforward way is using vg deconstruct -a {vg_graph.gbz} > {variants_in_graph.vcf}. The variants can be refered back to the input vcf based on the position and REF/ALT alleles. Note that the variant ID is modified in the graph.