Question: How to calculate linkage disequilibrium (LD) with only two genomes?
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gravatar for KL_STKLBK
3 months ago by
KL_STKLBK0
KL_STKLBK0 wrote:

I have a dataset of resequenced genomes for many populations yet only with two individuals per population. I would now like to compare patterns of linkage disequilibrium (LD) across populations. I already used the correlated zygosity statistics for single genomes that was developped by Lynch et al. 2014 and for which the software mlRho exists. However, I was wondering if there is any solution to calculate more conventional estimates for LD? Neither PLINK nor VCFtools seem to be able to handle this.

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