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
For PCA, the well-known Novembre 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)"
Thank you for your reply,
So, Can I use the data generated with the same parameters for admixture's input?
Hi, yes you can use the data for admixture analysis
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