is there a Quick way to link variants in a VCF to Genetic Testing Registry
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7.6 years ago
Rm 8.2k
  1. Through Clinvar CLNSRCID, any others?

I could not find the data download link regarding variants from GTR?

VCF GTR Clinvar • 1.7k views
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Entering edit mode
7.6 years ago

See http://www.ncbi.nlm.nih.gov/variation/docs/human_variation_vcf/#clinvar

This file contains variations submitted through clinical channels. The variations contained in this file are therefore a mixture of variations asserted to be pathogenic as well as those known to be non-pathogenic (see Note below). The user should note that any variant may have different assertions regarding clinical significance and that this file will contain only those that are the most "pathogenic".

You can use this file to fill the column ID of your VCF, with GATK for example

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