ClinVar namespaced variant data export#684
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jstone-dev wants to merge 3 commits intorelease-2026.1.2from
Open
ClinVar namespaced variant data export#684jstone-dev wants to merge 3 commits intorelease-2026.1.2from
jstone-dev wants to merge 3 commits intorelease-2026.1.2from
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This pull request adds support for exporting ClinVar data alongside variant information in the score set CSV export endpoint. It introduces a new namespace pattern for ClinVar-versioned data (e.g.,
clinvar.2024_01), allowing users to request multiple ClinVar versions simultaneously. The changes update the API, CSV generation logic, and documentation to handle these new namespaces and ensure correct column naming and data retrieval.ClinVar namespace support and CSV export enhancements:
clinvar.2024_01) in the CSV export endpoint, including validation of requested namespaces and documentation updates insrc/mavedb/routers/score_sets.py. [1] [2] [3] [4] [5]get_score_set_variants_as_csv,variant_to_csv_row,variants_to_csv_rows) to fetch and include per-variant ClinVar data, with proper column naming to avoid collisions when multiple ClinVar versions are requested. [1] [2] [3] [4] [5] [6] [7] [8] [9] [10]Internal and testing improvements:
These changes collectively enable users to export variant data with ClinVar annotations for multiple versions, improving clinical relevance and flexibility for downstream analyses.