How do I identify the REF from a VCF

[hyanwong]

When I use cyvcf2, I can access a variant.REF value, but I can't find any obvious references to the word "REF" in the Sgkit docs, for looking at a VCF read in with vcf_to_zarr. I assume that the first in the variant_alleles array is the vcf REF: is that guaranteed, and if so, can it be documented?

[tomwhite]

Yes, it is guaranteed. The format is documented here: https://github.com/pystatgen/vcf-zarr-spec/blob/main/vcf_zarr_spec.md, where it says:

Note that the REF and ALT fields are combined into a single Zarr array.

[hyanwong]

Thanks. Is it worth noting that in SGkit somewhere too? By my nitpicky reading of the docs, it doesn't say that they are combine with REF first, either (just that they are "combined")?

[tomwhite]

Very true! Are you interested in contributing a patch to fix these issues?

[hyanwong]

I'm happy to do so.