Pruning With Plink Variance Inflation Factor (--Indep) Vs. Pairwise Genotipic Correlation (--Indep-Pairwise).

Question

[makaonte]

Hi everybody,

I need to make some pruning with different R squared (0.5, 0.2, 0.01). Data is in plink format. That was ok I used the flag --indep-pairwise 50 5 0.01, but using --indep 50 5 0.01 I got twice as much SNPs in output. Why so big difference?