haplotype association with quantitative traits

Question

[kumar.vinod81]

I have a done a GWAS study in plant for quantitative trait and found some regions higly significant. Now, I want to see the haplotye structure around these SNPs and their reassociation with the trait so, I can capture the contributing haplotype. Does anyone know any tool which can make it possible? Thanks

Answer 1

[Floris Brenk]

Using plink:

First create haploblocks: http://pngu.mgh.harvard.edu/~purcell/plink/ld.shtml#blox

plink --bfile mydata --blocks (adding your region of interest)

Then test for association: http://pngu.mgh.harvard.edu/~purcell/plink/haplo.shtml#hap3

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

[kumar.vinod81]

Thanks Floris, But I am not able to use --blocks output as myfile.hlist as both are quite different. Do you have any idea? thanks for your help