Assigning haplotypes to individuals

Question

[Floris Brenk]

Hi all,

I have a large genotype dataset and using this I created haplotypes and haploblocks in plink (http://pngu.mgh.harvard.edu/~purcell/plink/haplo.shtml). Now I want to assign these haplotypes to the individuals and to do some manual eQTL analyses. Does anyone know whether this is possible in plink or other software?

Like output (or similar): Sample1 haplo1/haplo4 Sample2 haplo2/haplo2 etc.

Answer 1

[Floris Brenk]

Solved :)

http://pngu.mgh.harvard.edu/~purcell/plink/haplo.shtml#hap5

plink --file mydata --hap myfile.hlist --hap-phase