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. 2022 Apr 11;54(4):518–525. doi: 10.1038/s41588-022-01043-w

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© The Author(s) 2022

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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Extended Data Fig. 3 — Weighted genotype concordance at different coverages for sample NA12878. We ran PanGenie, BayesTyper, Paragraph, Platypus, GATK, GraphTyper and Giraffe in order to re-genotype all callset variants. Besides not applying any filter on the reported genotype qualities (‘all’), we additionally report genotyping statistics for PanGenie when using ‘high-gq’ filtering (genotype quality 200). SNPs, insertions and deletions include all respective variants in biallelic regions of the genome, while complex contains all variant alleles falling into regions with complex bubbles in the pangenome graph representation.