Question: (Closed) Post Imputation Analysis
1
gravatar for mandar.bobade60
5.6 years ago by
Bangalore
mandar.bobade6080 wrote:

Hi,

I am doing Genome-Wide Association Study data analysis. So far, before imputaion, QC analysis, association analysis, Imputation went well (of course with great efforts). But, after imputation I am quiet like confused, as I have done my imputation with Impute2. I have converted files from Impute2 output to PLINK output and also done dosage analysis.

But with literature survey, I am getting confused whether or not I can use PLINK for post-Imputation data. As, most of the papers are mentioning SNPTEST is meant for data analysis after imputation with Impute2. And I did it too, but if I see output of SNPTEST, I am hardly getting anything from it's output. Eventually leads, as per me, to stick with PLINK.

So my specific question is, shall I stick with PLINK analysis for Impute2 imputed data? If not, how to interpret SNPTEST output, especially Bayesian statistics output?

gwas imputation plink • 3.2k views
ADD COMMENTlink modified 5.1 years ago by Biostar ♦♦ 20 • written 5.6 years ago by mandar.bobade6080
1

See this post: How to analyze imputed GWAS data

ADD REPLYlink written 5.6 years ago by zx87548.2k

Hello mandar.bobade60!

We believe that this post does not fit the main topic of this site.

How To Analyze Imputed Gwas Data

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 2.4 years ago by zx87548.2k
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