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. 2023 May 12;24:197. doi: 10.1186/s12859-023-05294-0

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© The Author(s) 2023

Open AccessThis 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/. 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 in a credit line to the data.

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Fig. 3 — HG003 WGS variant calling results, annotated with 1000Genomes allele frequencies. a Variants are stratified by commonness. Left: common variants (allele frequency >0.01), right: rare variants (allele frequency $\leq$ 0.01). b, c Caller-specific errors by DeepVariant and DeepVariant-AF using 35x HG003 WGS data. Errors specific to DeepVariant are considered to be population-resolved, and the others are considered to be population-induced. b False positives (DeepVariant: 2085, DeepVariant-AF: 1070), c false negatives (DeepVariant: 2284, DeepVariant-AF: 1952)