Return reference calls with `vg calls`

Question

[Felix Bemm]

How would one call reference bases with vg call at the moment as such that they appear as 0/0 if read alignments support it? vg call had an option in 1.17 if I remember correctly but that disappeared in 1.19, Would vg genotype be one way?

Thanks, Felix

[Asaf]

Please edit your question so users (which are apparently not vg-Team) would be able to help you.

[Felix Bemm]

I think in this case only the vg team can help me.

[Felix Bemm]

I am running genotype like that:

./vg genotype -p -t 20 -v -r "path1" -V sample.vcf -E -G sample.fil.gam sample.aug.vg > sample.recall.vcf

sample.vcf is from vg call sample.fil.gam is an augmented filtered gam sample.aug.vg is the augmented graph

vg genotype works but the process takes huge amounts of memory for a pretty small graph. The graph is not from the vcf, its a genome alignment graph.

And it seems as genotype is not adding the path id to the vcf header.

Answer 1

[glenn.hickey]

Yeah, that option got lost when vg call was refactored (it didn't work very well). Please file a github issue to ask for it back.

But vg call can genotype a given VCF with the -v option, if the graph was constructed from that VCF with vg construct -a. This will produce 0/0 calls.