Hi,

Sorry if this is a silly question. I created a polygenic risk score for a disease. As a sensitivity analysis, I removed SNPs associated with education and reclumped the SNPs. Now, I get more SNPs in the .bim file with the clumped SNPs(without education) than the original anlaysis even though I removed more SNPs. Does this make sense? I checked to see if the education SNPs are in the .bim file but they aren't so I am assuming they have been removed. I'm wonder why I am getting a higher number of SNPs now? Is this related to how SNPs are clumped now? Would really appreciate if anyone has any idea?

Thanks