Question: How to analyze Exome Seq data for GWAS
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gravatar for Manoj
6 weeks ago by
Manoj80
United States
Manoj80 wrote:

Hi, I have got exome seq data from Ion Torrent platform. I am looking to analyze these data for GWAS studies. Please suggest pipelines and workflow.

gwas next-gen exome genome • 135 views
ADD COMMENTlink modified 6 weeks ago by Kevin Blighe65k • written 6 weeks ago by Manoj80
0
gravatar for Kevin Blighe
6 weeks ago by
Kevin Blighe65k
Kevin Blighe65k wrote:

Hey Manoj,

You could produce VCFs (or BCFs) and then import these to PLINK, where you could then perform standard GWAS analyses. There are 2 related answers, here: Convert vcf phased data to plink

If you have Ion Torrent data, I see no reason why you could not use GATK ( a related question, with no answer: NGS preprocessing pipleine for ion torrent data )

Kevin

ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by Kevin Blighe65k
1

That is awesome. It is good for my initial starting and understanding the GWAS studies.

ADD REPLYlink written 5 weeks ago by Manoj80

Hi Kevin, Thank you for your answer. You mentioned that "standard GWAS analysis". Could you elaborate your answer, what would be standard GWAS analysis. I am pretty new in GWAS analysis.

ADD REPLYlink written 5 weeks ago by Manoj80

Hey Manoj, well, it really depends on what you want to do. Usually, people are studying some disease and they want to find inherited genetic variants that are statistically significantly associated with the disease. A typical GWAS is actually just a basic chi-squared test on a 2 x 2 contingency table, comprising the 'mutant' allele and reference allele tallies in the cases and controls. I go through the basic calculations for this here: A: SNP dataset and Z Score (technically, you don't need PLINK).

If you are studying a condition like arthritis, heart disease, or something along these lines, it's imperative that you have a solid study design and that your study is Powered (statistically) so that you can make inferences to the wider population.

ADD REPLYlink written 5 weeks ago by Kevin Blighe65k
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