Fig. 2
From: Haplotype threading: accurate polyploid phasing from long reads
Overview of WHATSHAP POLYPHASE. The input allele matrix results from a given BAM and VCF file and an optional realignment step. Phase I: statistical scoring of each read pair classifies them into belonging to the same or to different haplotypes. The scores are used as weights for a graph over all reads, which is clustered by cluster editing (gray round shapes). Phase II threads k haplotypes (colored lines) through the clusters (here k=4) balancing coverage violations and switch costs while respecting the genotype information. This results in k phased haplotypes, subdivided into blocks (vertical lines)