Question: Analyze a set of sequences to obtain a genotype matrix (SNPs)
gravatar for tutoring891
5.4 years ago by
United States
tutoring8910 wrote:

Hello I have a set of 10 genomic sequences each corresponding to a sample. My final goal is to do Genome wide association analysis between a phenotype that I have for all the samples and the genotype (which is going to be obtained from the SNP data). I have the phenotypic trait value for each sample however I need also the genotypic data (SNPs) for those samples. In other words I would need a SNP matrix of size (10 * number of loci or sites). I'm not familiar at all in identifying or analyzing SNPs from those genomic sequences therefore I would really appreciate it if you could provide me assistance in terms of how would I convert a set of 10 genomic sequences into this genotypic matrix? I would appreciate it if you know a good R package which could assist me in doing this?



I also have a file of this form:

4 7291472 C G
4 7292641 A C
4 7302012 C T
4 7302344 A T
4 7315419 G C
4 7319414 C T
4 7344281 A C



Note sure how to use this file when calling for SNPs


snp • 1.7k views
ADD COMMENTlink modified 5.4 years ago by Fotis T30 • written 5.4 years ago by tutoring8910

It looks like SNPs have already been called and your file is the result of the calling?  Just an aside, 10 samples will not result in any meaningful results for "GWAS", as your power is at or near zero.  Do you have more samples?

ADD REPLYlink written 5.4 years ago by Sean Davis26k

Yes I have more samples. What is confusing to me is how I compute the SNP scores? Ultimately, I want to go through each loci and do association analysis w.r.t the phenotype of interest that I have... 

ADD REPLYlink written 5.4 years ago by tutoring8910

By "SNP scores" do you mean their quality or do you simply mean compiling all of the samples into a single matrix?

ADD REPLYlink written 5.4 years ago by Devon Ryan94k

Putting all samples into a single matrix...

ADD REPLYlink written 5.4 years ago by tutoring8910
gravatar for Fotis T
5.4 years ago by
Fotis T30
Democritus University of Thrace, Greece
Fotis T30 wrote:

I would advise you to use plink for your study. It is really well-documented and has everything you need. It is not an R package though.

Here is a guide on how you need to format the data for the program to accept it (ped and map format):

I can help you through it, if you need anything more.

ADD COMMENTlink written 5.4 years ago by Fotis T30
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