To test the performance of our method on unphased data, we performed the hyperparameter optimization described above for each population with genotype data from diploid individuals. We then tested our method on the same benchmarking data mentioned earlier using the optimal hyperparameters for CEU. The results are presented in fig. S8, which also shows a scatterplot of the inferred recombination rates compared to the true recombination rates for both phased and unphased data. Both settings are fairly unbiased for all but the smallest recombination rates. For the most part, inference using unphased individuals results in performance indistinguishable from that on perfectly phased data. As such, we recommend using genotype calls when phasing may be inaccurate.

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