Considering your example G1 = A and G2 = T, here is how you can calculate allele frequency from genotype counts:

A freq = (2 AA + AT) / 2 n

T freq = (2 TT + AT) / 2 n

i.e. if AA=65, AT=83, TT=35

A freq = [(2 * 65) + 83] / (2 * 183) = (130 + 83) / 366 = 213 / 366

A freq = 0.5819

Hope it helps

Thank Luis for your answer. I need to have a table of allele frequency instead of SNP data and I have 105000 SNPs and  371 genotypes. G1 in my example  is a genotype 1. So, instead of having two alleles for each locus (one allele per genotype), I want to have their allele frequencies (the allele frequency in each genotype).

I hope you get my idea.

For your situation I think the above stated suggestion of Anna Wolc is the fastest way. Is the same principle but applied for a larger scale analysis (such as yours).

GenAlex has routines for importing SNP data and once you have them there is easy to ask for the allele frequencies

Dear all,

thank you for your answers. I was able to solve it using  combine formulas and substitute in excel

Pablo: I know that genalex  can estimate the AF but I need to replace all SNP data with allele frequency