On duos and trios this method will agree perfectly with Merlin at sites that Merlin can phase. This introduces a possible confounding effect when using the Merlin haplotypes as the truth, as any errors in the Merlin haplotypes will not be detectable when compared to the Beagle duo/trio method. We show below using simulated data that Merlin is quite sensitive to genotyping error and that this does result in elevated switch errors. For this reason we only consider pedigrees that are more complex than a parent-child duo or father-mother-child trio when comparing methods. Larger pedigrees also give Merlin better ability to remove genotyping errors yielding more accurate validation haplotypes.
