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. 2019 Jun 3;20:116. doi: 10.1186/s13059-019-1709-0

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© The Author(s) 2019

Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License(http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Fig. 8 — Genotyping HMM. Colored states correspond to bipartitions of reads and allele assignments at that position. States in C₁ and C₂ correspond to bipartitions of reads covering positions 1 and 2 or 2 and 3, respectively. In order to compute genotype likelihoods after running the forward-backward algorithm, states of the same color have to be summed up in each column