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monarch-initiative / genophenocorr

Genotype Phenotype Correlation
https://monarch-initiative.github.io/genophenocorr/stable
MIT License
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varcode #1

Closed pnrobinson closed 1 year ago

pnrobinson commented 1 year ago

Explore varcode https://github.com/openvax/varcode

  1. Get some variants from ClinVar, e.g. https://www.ncbi.nlm.nih.gov/clinvar/?gr=0&term=FBN1%5Bgene%5D&redir=gene
  2. Code these variants as VCF representations, e.g. https://www.ncbi.nlm.nih.gov/clinvar/variation/1071312/?new_evidence=true, e.g, NC_000015.10:g.48412738C>A chr10, pos 48412738, ref C, alt A
  3. Get corresponding transcript representation from varcode, compare with gld standard in ClinVar
lnrekerle commented 1 year ago

Got varcode to work and it is able to assign variation effects to variants @pnrobinson

pnrobinson commented 1 year ago

thanks looks great!