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 !
•
written
by
David_emir
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:
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.
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?
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/
Thanks a lot for your assistance. right now i have done QC' ing using PLINK, for my Geno-typed data. I was looking for conducting Gender stratification, I have the following concerns/doubts which i am not able to solve. It would be great if you guys help me out.
1 - Gender stratification, if p values is consistently low, even on statistical correction, what can be done ? 2- How to Overlay MY SNP data with other major studies (Case control studies), and is their any databases where the genotype data is stored? 3- I have the Geno typed data with me, what all the other analysis can be done on it ?
I know this might be very silly questions, for a novice like me ......... its worth millions ! i am really feeling the heat of it. so, sorry for annoyance (in case)
Thanks a lot for your help !
Log in to answer this question.
