Use PLINK2 to extract the specific variants

Question

[wangdp123]

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

Answer 1

[chrchang523]

If you don't care about the rsIDs, you can just create new IDs with e.g. --set-all-var-ids.