Calculate minor allele frequencies with effect allele frequencies in GWAS
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2.2 years ago
rk ▴ 30

Hi,

I just wanted to check that I am thinking about the right way. My final aim is to convert z-scores to betas for my GWAS. I need the minor allele frequencies for my SNPs for the equation to convert z-scores to betas but I only have effect allele frequencies in my GWAS.

Wouldn't the minor allele frequency just be (Assuming biallelic SNPS):

1 - effectallelefreq if A1freq>0.5 and maf=eaf if eaf<0.5


Thank you!

SNP gwas maf • 1.4k views
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Logic looks OK to me.