the phasing accuracy should increase with the sample size; in standard practice, most imputation methods gain phasing information about each study individual only from the reference panel, and phasing accuracy does not depend on the size of the study sample. (This description applies to imputation methods based on hidden Markov models, or “HMMs” [6],[11]; non-HMM methods often discard other kinds of information.) The BEAGLE imputation model [12],[13] is one notable exception to this point, and we discuss its alternative modeling strategy in detail in this work.
