Good value of r2 in pruned data
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6.6 years ago
nagaramajdi ▴ 10

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

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6.6 years ago
Adam ★ 1.0k

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)"

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2735096/

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6.6 years ago
nagaramajdi ▴ 10

Thank you for your reply,

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

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Hi, yes you can use the data for admixture analysis

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