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Good value of r2 in pruned data

Hi everybody,

Could you please inform me about the good value of r2 to construct the pruned data in order to perform Admixture and PCA analyses?

I used plink command line --indep-pairwise 50 10 0.5

Thanks,

Majdi

snp
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updated by mark77529 • mark77529 • written by nagaramajdi • nagaramajdi

1 answer

For PCA, the well-known November 2008 paper used the following:

First, before running PCA we used the PLINK software to exclude SNPs with pairwise genotypic r2 greater than 80% within sliding windows of 50 SNPs (with a 5-SNP increment between windows)

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updated by Ram Ram • written by Adam Adam

Thank you for your reply,

So, can I use the data generated with the same parameters for admixture's input?

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updated by Ram Ram • written by nagaramajdi • nagaramajdi

I would like to confirm about parameters following those from well-known November 2008 paper. So I would use "plink --file input_data --indep-pairwise 50 5 0.8". Is that correct?

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written by mark77529 • mark77529

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