Annotate vcf with AF, gene symbol, functional information
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Entering edit mode
5 months ago
bsmith030465 ▴ 200

Hi,

I wanted to annotate my vcf file with the following fields:

  1. Gene symbol
  2. Functional effect (stop-gain, frameshift etc.)
  3. Allele Frequency from Gnomad

I downloaded the gnomad vcf file (v 3.1) and tried to annotate my vcf with it (using snpeff/snpsift), but I could only see the allele frequency in the gnomad vcf file. Is there a downloadable vcf database that can provide me with the three fields above?

thanks!

vcf gnomad snpeff dbsnp • 339 views
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Entering edit mode

I would first suggest you read the snpEff documentation and follow it. If you're not familiar with it, you can also use VEP to perform this task

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