Ibs And Ibd Analysis In Plink (Gwas)

Question

[mandar.bobade60]

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

[zx8754]

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

[Matt Shirley]

Yes, this is basically what I should have answered.

Answer 1

[Matt Shirley]

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.