Question: Linkage Disequlibirum (R^2) = recombination?
gravatar for Adrian Pelin
5.0 years ago by
Adrian Pelin2.3k
Adrian Pelin2.3k wrote:


There are methods to calculate LD from unphased VCF data and it calculates r^2 in windows. What I do not understand is how can you estimate LD just from Allele Frequency data? Do you not need to know the phase so that you may tell if everything is in phase among your different samples or possibly you have recombination?



ngs r^2 vcf • 1.2k views
ADD COMMENTlink written 5.0 years ago by Adrian Pelin2.3k

Classic methods require phased data.  You can measure LD without phased genotypes, but you loose power.  for example site 1: A:A site 2: A:G.  You know the haplotypes are AG and AA.   In the case of site1: A:G ; site 2: A:G you have no power.  

ADD REPLYlink written 5.0 years ago by Zev.Kronenberg11k

So if in sample #1: site 1 = A:A; site 2 = A:G while in sample2: site 1 = A:A; site 2 = A:A then that increases R^2 and decreases LD?


Is it assumed that in this case recombination removed A:G?

ADD REPLYlink modified 5.0 years ago • written 5.0 years ago by Adrian Pelin2.3k
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