the reference panel with inferred target haplotypes (Online Methods); under this paradigm, reference-based phasing should always improve accuracy over cohort-based phasing. We also note that the Eagle1 algorithm was originally only implemented for cohort-based phasing; in this work, we have extended the implementation to reference-based phasing for the sake of comparison. Likewise, we have implemented a cohort-based version of Eagle2 that we also benchmark below.
