We tested the latest version of each method (as of August 2015) using its recommended parameter settings. For Eagle (v1.0), SHAPEIT v2 (r790), and Beagle (v4.0 r1399), no command line arguments were required beyond file paths and threading settings (10 computational threads). For HAPI-UR (v1.01), we set the maximum window size to 80 (as recommended based on genotyping density) and combined results from three parallel runs of the algorithm using different random seeds11.
