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. 2019 Nov 27;10:5402. doi: 10.1038/s41467-019-13341-9

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© The Author(s) 2019

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as 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 images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — Overview of data structure and workflow. a Example structural variants and their encoding in an acyclic graph structure. b Workflow for constructing a GraphTyper graph with SNPs, indels and SVs. SVs are detected from each sample independently and then merged across all the samples, such that SV sites of the same type and similar position and size are reported only once. SNPs and indels that are given as input into the graph construction can be detected using GraphTyper or obtained from a database.