Overview of Refphase algorithm.

a) Refphase creates a minimum consistent segmentation across the single-sample segmentations input for each tumour. b) In each segment in which at least one sample had allelic imbalance in the tumour input, an optimal reference sample for phasing is determined. c) The phasing of each reference sample is derived from its BAF. d) Phasing is then applied to the BAFs in all other samples which are not the reference. e) Allele-specific copy numbers are re-estimated for each sample utilising the reference phasing, and the most parsimonious phasing solution along each chromosome is then chosen in horizontal phasing optimization. f) In each segment, event categories relative to the input ploidy of the corresponding sample are defined using LogR values. g) Tumour-level events are called and intra-tumour heterogeneity metrics calculated.