Question

remove singletons in LD pruning in plink

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4.5 years ago

monaallouba • 0

Hello,

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

Thanks

LD pruning Plink singletons • 1.4k views

ADD COMMENT • link updated 4.5 years ago by chrchang523 10k • written 4.5 years ago by monaallouba • 0

score 0 · Answer 1 · 2019-10-30

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4.5 years ago

chrchang523 10k

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.

ADD COMMENT • link 4.5 years ago by chrchang523 10k