Question

Ibs And Ibd Analysis In Plink (Gwas)

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11.3 years ago

mandar.bobade60 ▴ 80

Hi all, I am doning GWAS for data which I have. For that I want to exclude or remove duplicated or related individuals as well as individuals of divergent ancestry. I am using Plink for this QC analysis and have used --indep-pairwise 50 5 and 0.5 criteria. I have got result file also but I am not able to interpret statistics involved in it. Can anybody guide me in this aspect?

Thanks in advance, Mandar

gwas plink statistics • 6.7k views

ADD COMMENT • link updated 11.3 years ago by Matt Shirley 10k • written 11.3 years ago by mandar.bobade60 ▴ 80

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This post might be helpful: How large would inbreeding coefficient be to be anomalous?

ADD REPLY • link 11.3 years ago by zx8754 12k

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Yes, this is basically what I should have answered.

ADD REPLY • link 11.3 years ago by Matt Shirley 10k

score 1 · Answer 1 · 2013-07-26

The --indep-pairwise function simply lists SNPs that are in linkage disequilibrium - that is highly correlated to each other. You can do what you describe using PLINK (see Pairwaise IBD estimation), although you might choose a more accurate and efficient whole-genome IBD estimation method such as kcoeff.

Disclaimer: I used to work in the lab where kcoeff was published.