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How do I identify the REF from a VCF #1170

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hyanwong opened this issue Jan 19, 2024 · 4 comments · May be fixed by #1175
Open

How do I identify the REF from a VCF #1170

hyanwong opened this issue Jan 19, 2024 · 4 comments · May be fixed by #1175

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

@hyanwong
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I'm happy to do so.

@hyanwong hyanwong linked a pull request Jan 22, 2024 that will close this issue
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Add getting REF to how_do_i hyanwong/sgkit
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@tomwhite @hyanwong