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clingen-data-model / clingen-hail-reports

Performs filtering against gnomAD and ClinVar datasets. Uses Hail to report records with a population FAF above certain thresholds by gene.
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Fix bug in gnomad-clinvar-af-revstatus.ipynb for missing gnomad values #4

Closed theferrit32 closed 3 years ago

theferrit32 commented 3 years ago

Example:

These two should be joined, but row 5591 in output has NA for gnomad values.

https://www.ncbi.nlm.nih.gov/clinvar/variation/5591/ https://gnomad.broadinstitute.org/variant/22-29121087-A-G

theferrit32 commented 3 years ago

This was due to GRCh38 build mismatches with clinvar GRCh37 VCF