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  1. Jalview
  2. JAL-3467

Annotate already loaded proteins and transcripts direct from Clinvar

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    Details

    • Type: New Feature
    • Status: In Progress
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: None
    • Labels:
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      Description

      NCBI Clinvar's web api provides the most up to date route for obtaining biomedically relevant mutation data, and often other sources lag behind (including ClinVar's own ftp site which provides VCF, etc).

      Full variant details for specific entries are available by eUtils:
      https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=clinvar&id=48074&rettype=variation

      It also looks like a VCF or TSV dump can be obtained for a gene.
      docs here: https://www.ncbi.nlm.nih.gov/clinvar/docs/maintenance_use/

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              Assignee:
              gmungoc Mungo Carstairs
              Reporter:
              jprocter James Procter
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                Created:
                Updated: