LD-prune with plink

发表于 
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plink-1.07/plink --noweb --file input --indep-pairwise 50 5 0.5 --out tmp1
plink-1.07/plink --noweb --file input --extract tmp1.prune.in --recode --out output

Linkage disequilibrium based SNP pruning

--indep-pairwise 50 5 0.5
--indep-pairwise 50 5 0.2

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