Hi all,

Plink has the function "Linkage disequilibrium based SNP pruning" which is `--indep 50 5 2`

where the 2 stands for the vif threshold (VIF is 1/(1-R^2)) which means in this case r2 = 0,50.

*So Linkage disequilibrium* is the non-random *association* of alleles. I'm a bit strugling what for example an r2 of 0.5 means and how plink calculates this. Does 0.5 just mean a correlation of 0.5 between two snps? Can anyone explain to me a bit more what this 0.5 actually mean in real numbers. For example when I have 100 samples how many snps need to be in perfect LD to reach a r2 of 0.5?