Categorical variant matching

ga4gh / gks-portal

MIT License

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Categorical variant matching #16

Open korikuzma opened 2 weeks ago

korikuzma commented 2 weeks ago

Submitter Name

Mrinal Thomas

Submitter Affiliation

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korikuzma commented 2 weeks ago

Afternoon session

ahwagner commented 2 weeks ago

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

Mrinal-Thomas-Epic commented 2 weeks ago

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.