feat: Script for tabular clinvar submission#624
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Work in progress script for ClinVar tabular file generation in a format appropriate for submission. Some outstanding questions remain to be resolved, specifically around the ontologies desired for submission and the handling of categorical scoring ranges.
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January 14, 2026 17:35
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This pull request adds a script that exports variants from a given score set URN into a CSV/TSV with appropriate format to submit to ClinVar.
Run the script with
A few outstanding questions remain:
Condition IDandCondition Value, we are generatingMedGenandC0012634(the generic 'disease' condition) for all score sets. We should verify this condition is appropriate.Assay Type, we should talk with ClinVar about their various allowed assay types shown here: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/functional_assay_types.txt. These assay types don't seem to have an appropriate ontology for certain assays in MaveDB, such as Label-Seq or VAMP-Seq.Molecular Phenotype Measured, we should talk with ClinVar about an appropriate ontology for the field. We should also ensure we have a robust decision tree for moving from our controlled keywords for molecular phenotype to whatever we decide on with ClinVar.methodandmethod citation.