How to get the refSNP ids or rsIDs of variants from UKbiobank datasets
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3.6 years ago
a.james ▴ 240

Dear All,

I have a list of variants from UKbiobank pipelines. Now, I need to annotate them with GWAS catalog, for that, I need the refSNP id or rsids. The current variants have no rsiDS for them. I would like to extract that, could someone please suggest something for that? I have seen Biomart, and VEP tool. In which I have tried VEP which does not provide the rsID. BioMaRT I have tried for a single chromosome. It threw memory error,

Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [www.ensembl.org:80] Operation timed out after 300000 milliseconds with 1413966 bytes received

Thanks! Any suggestions are much appreciated.

SNP sequencing genome next-gen • 960 views
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