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Categorical variant matching #16

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korikuzma opened this issue Nov 4, 2024 · 3 comments
Open

Categorical variant matching #16

korikuzma opened this issue Nov 4, 2024 · 3 comments
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Afternoon Session ASHG-2024 ASHG GKS Unconference 2024 Selected Tasks that were selected at the event and have followup attached to the issue

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Mrinal Thomas

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@korikuzma
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Afternoon session

@ahwagner ahwagner added the Selected Tasks that were selected at the event and have followup attached to the issue label Nov 4, 2024
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ahwagner commented Nov 4, 2024

Today's outcomes:

  • discovered challenges in setting up VRS Python on Windows machines (even in WSL)
  • future topic: finish dev containers etc.
  • copy number counts to constraints on shared genomic assembly
  • small variant (VCF) to categorical matching using VRS IDs
  • everything in Jupyter Notebooks

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Another future topic we discussed: performing matching in a database context, rather than just comparing single VRS variation to CatVar (e.g., with dataframe operations or a SQL query), since that may be inefficient for large numbers of variants. This will allow for predicate pushdown and use of indices.

@korikuzma korikuzma added ASHG-2024 ASHG GKS Unconference 2024 Afternoon Session labels Nov 7, 2024
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