snpgdsLDpruning for getting the number of independent markers for GWAS

[MuBulut]

Hi,
I was using the snpgdsLDpruning function to determine the actual number of independent SNPs in my genotype file, to perform BF correction for my GWAS. The function gives me a number of marker, which are selected (see fig. 24802 Markers).
My question: Is this the number of the independent Markers (BF = 0.05/24802), or is it the number of SNPs which are in LD (0.05/(3613062-24802))?

Thanks in advance.
M.

[zhengxwen]

It is the number of the approx. independent Markers.

[MuBulut]

nice thanks this helps a lot, and btw is there a way how to define/calculate the right sliding windows for calculating the numbers of independent markers?