Agreement between methods for the 20 lowest quality samples ranked by each algorithm. All methods agree on 18 samples, GenCall, Illuminus and CRLMM all agree on a further sample. CRLMM and Illuminus or GenoSNP and GenCall both agree on another sample each. The sample flagged by GenoSNP alone was ranked just outside the worst 20 samples by the other methods (22nd, 23rd and 25th for GenCall, Illuminus and CRLMM respectively). Plots of the raw signal from 3 samples ranked amongst the worst 20 by all methods are given in Additional File 1: Supplemental Figure S5.