Has anyone stored/queried VCFs and their variant records in a relational database?

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Gwas Genomics Genetics Vcf statistical-genetics

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  • sgkit

    We've moved to https://github.com/sgkit-dev/sgkit

    • I once built on top of a library that used the zarr format for storing the vcf data. It allowed me to parse over it like it was a pandas dataframe and incredibly fast. sgkit is the successor library and seems to be growing really well, but I haven't played with it. I do have high hopes for the zarr format, but I am biased

  • TileDB-VCF

    Efficient variant-call data storage and retrieval library using the TileDB storage library.

    • Perhaps of interest https://github.com/TileDB-Inc/TileDB-VCF

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    The modern identity platform for B2B SaaS. The APIs are flexible and easy-to-use, supporting authentication, user identity, and complex enterprise features like SSO and SCIM provisioning.

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