MLE Approach: Calculate LD (r^2) from unphased data

Question

[Adrian Pelin]

Hello,

I have several population samples, and was able to align my illumina reads to a reference genome and call variants.

I am interested to test whether the organism is asexual, and that would involve testing for LD. Since I don't have phased data, I used plink to calculate r^2 using dprime. It is an approach described here and uses MLE to estimate haplotype frequency.

Can someone help me understand how this approach tests for recombination? If in one sample you have 2 biallelic markers at frequency X and in the second sample you have the same frequency X for the same 2 bi allelic markers, that means that for those 2 SNPs no recombination is happening? Why would recombination change allele frequencies?

Adrian

[Zev.Kronenberg]

What is the ploidy of your organism? If you have an a-sexual organism you should be aware that the hill equation assumes Hardy-Weinberg, which wouldn't fit the data.