Filter duplicate ID from PLINK file

Question

[Sumeet]

Hi All,

I am new to SNP-chip data analysis.

I have been exploring some SNP-chip data using plink 1.9, while checking the Relatedness using KING, I am getting an error of duplicate ID.

I was wondering if there is any method I can remove the duplicate individuals and retain only one copy of the same at every first step (before QC).

Thank you,

Answer 1

[chrchang523]

You first need to edit your .fam file to assign unique IDs. After you've done that, you can follow up with e.g. plink's --extract or --exclude flag to select which samples you want to keep.