text: user2727: I am interested in 20 different SNPs that all are either As or Gs, and they all occur on the same chromosome. How can I assess the co-occurrence of these SNPs? In other words, I want to know, if SNP1 is "G", does that make SNP2 to be more likely to be a "G" as well?
  I know this is broad and I'm not looking for a script or anything so specific, just a point in the right direction. I'm working with a non-model organism, so any organism-specific application won't be useful without being able to learn the methodology.
  Googling thus far has only brought up GWAS and similar methods of correlating a genotype and a phenotype, but not within a genotype.
  
  user2727: I found the LDheatmap package in R very helpful at calculating linkage disequilibrium. You can make plots such as this:
  
  
original_text: 2727: <p>I am interested in 20 different SNPs that all are either As or Gs, and they all occur on the same chromosome. How can I assess the co-occurrence of these SNPs? In other words, I want to know, if SNP1 is "G", does that make SNP2 to be more likely to be a "G" as well?</p>
  
  <p>I know this is broad and I'm not looking for a script or anything so specific, just a point in the right direction. I'm working with a non-model organism, so any organism-specific application won't be useful without being able to learn the methodology.</p>
  
  <p>Googling thus far has only brought up GWAS and similar methods of correlating a genotype and a phenotype, but not within a genotype.</p>
   2727: <p>I found the <a href="https://cran.r-project.org/web/packages/LDheatmap/vignettes/LDheatmap.pdf" rel="nofollow noreferrer">LDheatmap</a> package in R very helpful at calculating linkage disequilibrium. You can make plots such as this:</p>
  
  <p><a href="https://i.stack.imgur.com/kexIy.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/kexIy.jpg" alt="enter image description here"></a></p>
  