How to calculate IBD for different ethnicity using plink
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6.2 years ago
MAPK ★ 2.0k

I have a multigenome vcf file with samples from different ethnicities. I have converted this file to .ped and .map formats to work with Plink. I want to calculate the IBD relationship of samples using Plink, but I don't know exactly how it works and how it takes the problem of population stratification into account while calculating IBD. Can someone please explain a bit on this. Thanks

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I don't think plink will take population stratification into account. You will have to adjust for it by carrying out population stratification analysis and isolating your population of interest. Plink can be used to carry out the population stratification (http://pngu.mgh.harvard.edu/~purcell/plink/strat.shtml) or you could also use SNPRelate (http://bioconductor.org/packages/release/bioc/vignettes/SNPRelate/inst/doc/SNPRelateTutorial.html)

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Thanks! Do you know how many SNPs Plink needs?

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I'm not sure. You could write to the authors they might be able to give you more concrete answers.