SACGF / SACGF/variantgrid

Think about storing Variants with "N" sequences

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#1,548 2 comments 0 reactions 1 assignee Claimed by @davmlaw View on GitHub
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Description

Currently we reject: `chr5 123456 AG GNAT`

With: "non-standard bases in ALT sequence"

I am not sure what to do in this case. In some ways, it's worth storing. But the annotation is going to be sparse/bad, and if someone else uploads the same variant in effect, but with the base filled in, then we won't have matched/linked them, and eg a common variant (and tag/classification etc) will be missed

I guess we don't have that now, as we reject it

Should probably see what VEP does with it. And liftover etc etc

Also, we could just display a warning on the variant page if it contains an N

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