Question: haplotype association with quantitative traits
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gravatar for kumar.vinod81
3.3 years ago by
kumar.vinod81280
New Delhi
kumar.vinod81280 wrote:

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

haplotype gwas • 1.5k views
ADD COMMENTlink modified 3.3 years ago by Floris Brenk890 • written 3.3 years ago by kumar.vinod81280
0
gravatar for Floris Brenk
3.3 years ago by
Floris Brenk890
USA
Floris Brenk890 wrote:

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

ADD COMMENTlink written 3.3 years ago by Floris Brenk890

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

ADD REPLYlink written 3.3 years ago by kumar.vinod81280
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