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ga4gh / gk-pilot

A pilot implementation of GKS Work Stream specifications.
Apache License 2.0
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What variations are in the ClinVar pilot set? #4

Open larrybabb opened 1 year ago

larrybabb commented 1 year ago

From (Epic) - Jan 4, 2023

  1. How did you decide which variations to include in the current sample data set?

  2. Is it possible to run your current transformation on all the nonstructural alleles from ClinVar?

larrybabb commented 1 year ago
  1. We selected any Variants in ClinVar that had a ClinGen VCEP SCV (3-star). But we bring in all the scvs for those variants.
  2. We are able to run our standardization transformer on all clinvar variation. In the gk pilot dataset we are able to create VRS Allele variations for anything that is an allele. However, most everything else will be transformed to Text variations. We will be working to get the CNVs, Genotypes and Haplotypes in their proper VRS form as the VRS spec for those classes get resolved for any major concerns. (I believe CNVs, Genotypes and Haplotypes should be transformable in Q1 2023.