Hypothetical question just to illustrate what I'm trying to do:
A small gene "FOOBAR" on human chromosome 1 has been genotyped last year for three SNPs (in a LD block) for a total 1000 unrelated Finnish samples. The following are the summarized genotypes. Sample_1's genotypes for these three SNPs are "AG", "AC" and "CT", respectively. What are the estimated haplotypes for Sample_1 and the haplotype's probabilities?
SNP1 SNP2 SNP3 TotalSample AA CC TT 160 GG AA CC 358 GG AA CT 2 AG AC CT 480