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Adding input assembly for gnomad vcf queries #490

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korikuzma opened this issue Aug 10, 2023 · 2 comments
Open

Adding input assembly for gnomad vcf queries #490

korikuzma opened this issue Aug 10, 2023 · 2 comments
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bug Something isn't working vrs-2-alpha Changes are needed for the `staging` branch which points to VRS 2.0-alpha

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@korikuzma
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This CIViC Variant (3-10191647-T-G) is valid on both GRCh38 and GRCh37. In the refactor, we try GRCh38 first. We then try GRCh37 if validation checks don't pass for GRCh38. If a user knows which assembly the gnomad vcf variant is in, they should be able to pass this option so that it gets the correct VRS ID. The default assembly name should be GRCh38

We are running CIViC variants in our manuscript analysis with refactor updates and I saw that the VRS ID changed.

@jsstevenson
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Is this relevant (like to ground a lookup) in any other search modes? Maybe we could do it in one pass for everywhere that it makes sense?

@korikuzma
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@jsstevenson I think it makes sense for free text genomic and gnomad vcf in /normalize. It doesn't matter in /to_vrs since it will return both representations

@korikuzma korikuzma self-assigned this Aug 15, 2023
@korikuzma korikuzma added the vrs-2-alpha Changes are needed for the `staging` branch which points to VRS 2.0-alpha label Sep 28, 2023
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bug Something isn't working vrs-2-alpha Changes are needed for the `staging` branch which points to VRS 2.0-alpha
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