I am trying to work on SNPs case-control studies. I am working on benign and malignant Melanoma samples and our goal is to differentiate benign and malignant by looking at SNPs. I just want to get SNPs list that are unique in malignant but not benign.I am using gPLINK but I am not sure whether I am using the correct analysis for my SNPs data. The samples are unrelated to each other. I will show the steps what I figured out so far is the way to do in gPLINK for my analysis.
- make bed files
- Quality control steps: MAF, GENO, MIND and HWE
- Again make bed file after filtering
- Association tests: Allelic association tests or logistic regression(not sure which one to use)
- look into p-values, OR ratio and/ chisquare values
- Manhattan plot- for significant snps
- LD plot( also not sure about this)
- What kind of association test I should do if I want to just look at phenotypic effects or just genotypic effects or both??
- Since those samples are unrelated to each other, I think I don't have to do stratification test right??
- In which case it is good to look at LD plot?
Really appreciate your help!!