ld-pruning to a specific number of SNPs

Question

[javadjamshidi]

Hi everyone,

I was wondering if there is a way to do the Ld-pruning to a specific number of SNPs. For example, I have 5 million SNPs and I want to prune the SNPs and keep only 1 million of them, rather than specifying a window size and r2.

Many thanks

Answer 1

[chrchang523]

This is not directly supported, but you can achieve the same effect by choosing an appropriate window size/r2 which yields slightly more SNPs, and then following up with plink --bfile <mostly-pruned dataset> --thin-count 1000000 --make-bed --out ....