feat: Script for tabular clinvar submission #624
Draft
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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.