We empirically determined a threshold on the Beagle posteriors in order to fix genotypes while maintaining relatively low discordance rates. This approach relies on the Beagle posteriors being well calibrated. To do so, we defined a set of 23 different threshold values ranging from 0.5 to 0.999 and measured for each (1) the discordance between CG1 and genotypes with a posterior above the threshold and (2) the percentage of genotypes with posteriors falling below the threshold (Supplementary Fig. 4a-b). In addition, we also measured the proportion of discordances of the full Beagle call set falling below each threshold value (Supplementary Fig. 4c-d). From this experiment, we empirically determined that a threshold value of 0.995 gives good performance: it implies that around 97% of the genotypes can be directly fixed while maintaining a discordance against CG1 of 0.07% overall (ALL) and of 0.25% at genotypes involving at least one alternative allele (ALT). We find that the 3% of the genotypes that we choose not to fix contain over 80% of the genotypes found to be discordant. Thus it makes sense that these are the genotypes that we try to improve upon using our model.
