calculating LD for SNPs with more than two alleles

Question

[Scott]

How can multi-allelic (more than two alleles) SNPs be dealt with in LD analysis? I have used Haploview and VCFtools and I know these SNPs are excluded from the analysis. Ideally I would like to include these SNPs. Are there ways to treat each as multiple SNPs with different combinations of the alleles, and are there tools or options that allow them to be included in the analysis?

Answer 1

[Adam]

Maybe the vcftools --geno-chisq option would meet your needs?

[Scott]

Hi Adam. Thanks for the suggestion. I'm not sure if this is what I am looking for. Does this compute pairwise Chi-squared for each allele in any given SNP, with other SNPs? If so, I'm not sure how to integrate this data with R^2. A thorough explanation of what this option does would be great. Thank you!

Answer 2

[Scott]

see comment