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.
https://link.springer.com/article/10.1007/s00439-011-1118-2
https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006889
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Abbas.M •
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You could prune your dataset with plink : https://www.cog-genomics.org/plink/1.9/ld and then count how many SNP are in the resulting plink.prune.in file.
In Anderson et al. 2010 good GWAS practices paper, to compute a pruned dataset : https://www.nature.com/articles/nprot.2010.116
plink --file raw-GWA-data --exclude high-LD-regions.txt --range --indep-pairwise 0.15 50 5 0.2 --out raw-GWA-data
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