LD pruning for PCA

[cuiping]

It is suggested to do LD pruning on the variants before running PCA. See here: https://groups.google.com/forum/#!topic/plink2-users/7mWhcP-Klx4
Highlight: "I think lack of LD pruning would matter if some of the statistically significant PCs turned out to reflect local LD rather than global structure induced by geography or lab artifacts. You probably would not want to partial out PCs that merely reflected LD. "

So how to do LD pruning?
See here: http://pngu.mgh.harvard.edu/~purcell/plink/summary.shtml#prune
We use the default LD r^2 value 0.5 as a cutoff: LD pruning < 0.5
plink --file data --indep-pairwise 50 5 0.5
the command above that specifies 50 5 0.5 would a) consider a window of 50 SNPs, b) calculate LD between each pair of SNPs in the window, b) remove one of a pair of SNPs if the LD is greater than 0.5, c) shift the window 5 SNPs forward and repeat the procedure.