Question: calculating LD for SNPs with more than two alleles
0
gravatar for Scott
4.8 years ago by
Scott80
Canada
Scott80 wrote:

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?

ADD COMMENTlink modified 4.7 years ago by Biostar ♦♦ 20 • written 4.8 years ago by Scott80
1
gravatar for Adam
4.8 years ago by
Adam990
United States
Adam990 wrote:

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

 

 

ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by Adam990

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! 

ADD REPLYlink written 4.8 years ago by Scott80
0
gravatar for Scott
4.8 years ago by
Scott80
Canada
Scott80 wrote:

see comment

ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by Scott80
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