By contrast, the recently published BEAGLE [13] imputation approach fits a full joint model to all individuals at all SNPs. To overcome the difficulties caused by the large space of possible genotype configurations, BEAGLE initializes its model using a few ad-hoc burn-in iterations in which genotype imputation is driven primarily by the reference panel. The intuition is that this burn-in period will help the model reach a plausible part of parameter space, which can be used as a starting point for fitting a full joint model.
