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. 2020 Oct 29;10:18542. doi: 10.1038/s41598-020-75387-w

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© The Author(s) 2020

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 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/.

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Effect of different settings on imputation accuracy evaluated by down-sampling NE1. (A) Performance using different genotype callers in a 0.05 × coverage genome; (B) Effect of pre-imputation filters in a 0.05 × coverage genome; (C) Effect of post-imputation filters at in a 0.05 × coverage genome; (D) Performance using different reference panels during the genotype probability update and imputation steps in a 0.05 × coverage genome. The inset on the top-right corner shows the proportion of heterozygous sites called in the original 20 × genome that are correctly imputed (i.e. not imputed as homozygous or failing the post-imputation filter). tv: transversion.