I am trying to construct haplotype genotype using PLINK (if not possible need to use other software). What I mean by halplotype genotype is two haplotype allele per individual (need to know phase to do that). The figure shows the concept. I know we can haplotype block construction using PLINK (see PLINK documentation).
plink --bfile mydata --blocks
But I do not know how to produce haplotype genotype from here. We can do a haplotype test using the following command, but without outputting halotype genotype. What I am trying to do is use the haplotype genotype information in other stastical softwares.
plink --file mydata --hap myfile.hlist --hap-assoc
Help is appreciated............. .. ..... .......... ...... .... ...... ......
Link for the figure, if it doesnot open here. haplotype genotype figure concept
