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LD pruning before imputation?

I'm new to imputation. And I filtered samples and markers before imputation. But I do not know, if I should filter SNPs by LD before imputation.

For example, use plink --indep-pairwise 50 1 0.75 to remove SNPs in high LD.

Can anyone explain why should I do that or not?

Thanks

snp plink impute ld
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updated by zx8754 zx8754 • written by whtopjazz • whtopjazz

There are tutorials/manuals online for imputation, pick one and follow through. (I wouldn't prune anything)

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written by zx8754 zx8754

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