Good value of r2 in pruned data

Question

[nagaramajdi]

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

Answer 1

[Adam]

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)

[nagaramajdi]

Thank you for your reply,

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

[mariaf.betancur]

Hi, yes you can use the data for admixture analysis

[mark77529]

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?