Question: How To Get Started Learning Gwas Analysis
9
gravatar for David_emir
5.9 years ago by
David_emir330
India
David_emir330 wrote:

Hello All,

I have a genotyping data from Human Omni 1 Quad v1.0 DNA Bead Chip with Demographic Particulars of Cases and Controls. Since i am very new to GWAS , it would be really helpful if you please let me know the ways for Conducting a full GWAS analysis of the raw data, for arriving at SNPs with different p-value (<0.005, < 0.001) data sets, how to have an Association analysis of imputed data and also have a pathway analysis from the SNP data to chart disease relevance.

It would be really helpful if you guys please let me know the pipeline for it and related tools for this analysis !

Thanks a lot for you help !

ADD COMMENTlink modified 5.8 years ago by Bioch'Ti1000 • written 5.9 years ago by David_emir330
16
gravatar for zx8754
5.9 years ago by
zx87547.3k
London
zx87547.3k wrote:

Following two papers with examples should get you started with GWAS QC and Analysis:

Data quality control in genetic case-control association studies

Basic statistical analysis in genetic case-control studies

EDIT: Starting point for Pathway analysis see:

Plink - Set-based tests

Plinkseq - Gene/group-based association tests

ADD COMMENTlink modified 5.8 years ago • written 5.9 years ago by zx87547.3k
1

These two are very good papers for starters to understand statistics and its use in GWAS QC. Thanks a lot for this suggestion. It was very useful.

ADD REPLYlink written 5.8 years ago by mandar.bobade6080

Thanks a lot for your help, Its really useful.. I have a doubt, Is it possible for arriving pathway-based analysis, report from the derived SNPs?

ADD REPLYlink written 5.8 years ago by David_emir330

See edited answer. Please avoid asking extra questions in comments.

ADD REPLYlink written 5.8 years ago by zx87547.3k
2
gravatar for Bioch'Ti
5.8 years ago by
Bioch'Ti1000
France (Avignon)
Bioch'Ti1000 wrote:

Hi, you may also been interested in using the Tassel Saftware that implements the Mixed Linear Model. There is some support to its use. Visit: http://www.maizegenetics.net/tassel/

ADD COMMENTlink modified 5.8 years ago • written 5.8 years ago by Bioch'Ti1000
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