GWAS: I only have information on single allele in every samples. Example: At pos 657, sample 1 has T, sample 2 has C, sample3 has T and so on. To conduct a GWAS, should I consider it as homozygous? Ex. C should be treated as CC for position 657 in sample2. T as TT in sample1 and sample3.
How should I approach to analyze this kind of data? Substituting As homozygous (C as CC) then running normal GWAS is what I have done. If anyone has alternating ideas i would be grateful.