Hi,

Can vg deconstruct or any other vg/minigraph-cactus tool export a GATK-style all-sites gVCF from a pangenome graph?

I understand that vg deconstruct creates VCF records for snarls/bubbles in the graph, with REF/ALT alleles derived from graph paths. This gives a sparse graph-derived variant VCF. However, I need to know whether positions absent from the exported VCF can be interpreted as reference, missing, or not comparable for each path.

Is there a supported workflow to obtain an all-sites gVCF-like representation from a graph, or should graph-derived VCFs be treated only as variant-site VCFs?

Thanks!