Hi, everyone. I am a fourth-year statistics student who has a great passion and interest in Statistical Genetics and Genomics. I am trying a small imputation project by myself, but I encounter a problem. I want to assess the accuracy of FastPhase imputation with a small number of SNP. But I am not very familiar with the dataset format.

I downloaded the SNPs for Chromosome 6 (tab-delimited text file): The following is the first 6 rows:

137505903-IL22RA2-6 D001    c   c
137505903-IL22RA2-6 D002    c   c
137505903-IL22RA2-6 D003    c   c
137505903-IL22RA2-6 D004    c   c
137505903-IL22RA2-6 D005    c   c
137505903-IL22RA2-6 D006    c   c

On the website it writes: Line format:

<chromosome position-HUGO_NAME-chromosome > <PGA Sample ID> <Allele1> <Allele2>

But then I am confused about how could I convert it into the fast phase input format. How could I know which one is 0 and which one is 1, I know that Homozygous:0, Heterozygote,1 homozygous for the less frequent allele,2. But I am not sure how to determine here and I am confused with there is only Allele1 and Allele2 but not something like 0,1,0,1,1,1,0, .. (a string).

Thank you so much.