Question: Use PLINK2 to extract the specific variants
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gravatar for wangdp123
13 days ago by
wangdp123240
Oxford
wangdp123240 wrote:

Hi there,

I am attempting to use PLINK2 with its --extract flag to extract the specific set of variants from UK Biobank dataset in *.bgen format. Unfortunately, the variant IDs contained in .bgen file is in rs_id format, which is not unique.

For example, the two different SNPs happening in the same locus will be given the exactly the same rs_id. But I only want to extract the information for one of them.

I wonder if there is a way to ask PLINK2 to extract the variants not only based on the variant ID but also by the Allele1 and Allele2 information?

Many thanks,

Tom

plink2 • 65 views
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