MLE Approach: Calculate LD (r^2) from unphased data
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6.6 years ago
Adrian Pelin ★ 2.4k

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 "http://www.biomedcentral.com/1471-2105/8/428" 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

 

 

 

LD r^2 vcf plink • 2.5k views
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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. 

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