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