To perform cohort-based phasing (i.e., without a reference), Eagle2 employs an iteration similar to the above approach, but prior to running two iterations of the Eagle2 core phasing algorithm as described above, it first runs the first two steps of the Eagle1 algorithm, which rapidly detect identical-by-descent segments and use them to call phase13. Within small data sets, identity-by-descent is less common, but our results indicate that the two subsequent iterations of the Eagle2 core phasing algorithm are able to rapidly refine phase calls given even an inaccurate set of initial phase calls.
