I am pruning datasets of varying SNP density using PLINK --indep-pairwise, comparing different r2 cut-offs. The density ranges from the 1000 Genomes phase 3 data (e.g. >6 million SNPs on chr 2) to that of SNP-array data (20.000 SNPs on chr 2). While doing so, I want to keep the other parameters (window-size and frame-shift) constant.
My current parameter choices are: --indep-pairwise 10000 1000 [r2-cut-off, which varies in a range from 0.5-0.95]
Is there a downside to choosing a large window-size like 10000 on less dense data or a high r2-cut-off other than run-time?