How to delete Duplicate snps in plink 1.9

Question

[xuyang]

Hello guys, I am new for plink 1.9 and recently I met an error with duplicate snps in my .bim file. I tried using --exclude to delete them and it deleting all matches, but I also need one of them to stay in the dataset. Is there any other available command line for dealing with duplicate snps? Thank you so much!

Answer 1

[chrchang523]

It's only implemented in plink 2.0 rather than 1.9, but the --rm-dup flag (https://www.cog-genomics.org/plink/2.0/filter#rm_dup ) should do what you need.