remove singletons in LD pruning in plink

Question

[monaallouba]

Hello,

How can I remove singletons in LD pruning in plink?Is there a specific command for that?

Thanks

Answer 1

[chrchang523]

This is independent of LD pruning, you’d want to do it beforehand.

plink —bfile ... —mac 2 —make-bed —out ...

removes all singleton heterozygous variants.