Forum: What is the better association analysis to use for SNPs using gPLINK?
gravatar for kc
4.8 years ago by
United States
kc20 wrote:

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.

  1. make bed files 
  2. Quality control steps: MAF, GENO, MIND and HWE
  3. Again make bed file after filtering
  4. Association tests: Allelic association tests or logistic regression(not sure which one to use)
  5. look into p-values, OR ratio and/ chisquare values​
  6. Manhattan plot- for significant snps
  7. LD plot( also not sure about this)



  1. What kind of association test I should do if I want to just look at phenotypic effects or just genotypic effects or both??
  2. Since those samples are unrelated to each other, I think I don't have to do stratification test right??
  3. In which case it is good to look at LD plot?


Really appreciate your help!!

snp plink forum • 2.0k views
ADD COMMENTlink modified 4.8 years ago by RamRS25k • written 4.8 years ago by kc20
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 864 users visited in the last hour