remove singletons in LD pruning in plink
Hello,
How can I remove singletons in LD pruning in plink?Is there a specific command for that?
Thanks
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chrchang523
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monaallouba •
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monaallouba •
1 answer
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.
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