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!
calculating LD for SNPs with more than two alleles
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?
2 answers
Log in to answer this question.
More posts like this
-
Why remove multiallelic sites ?
written by Andrea Catalina •
-
Tool that can merge 2 VCF files while taking "representational ambiguity" of (multi-allelic) varian…
written by William
-
What is optimal distance to scan for genes near SNPs for pathway overrepresentation analysis?
written by rimgubaev
-
LD between CNVs and exterior SNPs
written by Ana
-
Vcftools r2 Error: Insufficient sites remained after filtering or No data left for analysis!
written by hellbio
-
LD Analysis between SNPs and CNVs
written by Nev •
-
VCFtools LD calculations only for pairs that include a single SNP of interest
written by Scott
-
Which Is The Best Way For Filtering A Vcf File For Only Variation Sites?
written by dapregi •
-
Haplotype Vs Multilocus Test
written by Varun •
-
Is Haploview The Best Method For Defining Ld Blocks?
written by User 7433 •
