Question: Haplotype Genotype (Two Haplotype Alleles) Estimation In Plink Or Any Other Software
gravatar for John
8.7 years ago by
John1.5k wrote:

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............. .. ..... .......... ...... .... ...... ......

haplotype genotype

Link for the figure, if it doesnot open here. haplotype genotype figure concept

haplotype plink genotyping • 4.5k views
ADD COMMENTlink modified 6.7 years ago by Biostar ♦♦ 20 • written 8.7 years ago by John1.5k
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