I want to set a threshold of GWAS based on effect number of independent snps in my genotype data. As i read in literature, most of the recently published papers have set threshold by this way. At first they calculated effective number of independent snps in their snp data. Then applied a basic bonferroni correction. Lets suppose, if effective number of independent markers are 20000 then the threshold would be like this, 0.05/20000, here 0.05 is the 5% error rate. Genetic type 1 error calculator can do it, but their website is unstable and i am unable to access it. Is there any alternative methods to estimate independent number of markers in a SNP data? Here is the link of the paper, in which they proposed this method, and other studies using their proposed method.