How to get the number of significant loci from GWAS

Question

[YL]

I know this is a very basic question. I have a GWAS dataset with thousands of significant SNPs. I know we can see roughly how many loci from visualizing the Manhattan plot or manually reviewing the locations. But I wonder how I could automatically get the number of significant loci?

Thank you very much!

[4galaxy77]

Do you want to know how many independent loci? I.e. you have multiple SNPs per region/loci? You could do LD clumping using plink if so

[YL]

Thank you so much! I wonder if you have any recommended parameter settings? I tried to default setting and it dose not seem to perform well (still hundreds of loci......)