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. 2019 Aug 29;10:3908. doi: 10.1038/s41467-019-11857-8

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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. 4 — SCAN-SNV workflow. GATK HaplotypeCaller determines sites with non-reference evidence and discovers germline or clonal hSNPs from bulk. Phased hSNPs serve as a training set to learn AB correlation patterns, predict AB at candidate sSNV loci and estimate artifact prevalence. Only candidate sSNVs passing all filters are reported as putative mutations