Provide small example file. It is usually easy to convert almost any file to plink format.

Dear Tokhir,

The file is like:

            ind1   ind2     ind3  ......

snp1    0          1          2

snp2     2          1          1

.

.

.

here the ind1.... are individuals.

Thank you.

f2= sum(each num. by row)/(2* #individulas)

You will get the allele fre. of the second allele (denoted as f2)

if f2

Thank you Zhe.

Here is another question: If A1/A2 alleles are there, but I did not know A1 is reference or alternative allele. How could I confirm which column is ref/alt? From vcf file, it is obvious. But I do not have that file.

Thank you.

MAF=(2*Ref. allele)/(2*(Ref.allele + alternate. allele))