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. 2019 Jun 27;9:9345. doi: 10.1038/s41598-019-45835-3

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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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Variant calling runtime of multiple combinations in WES datasets. The variant calling runtime of each combination run on a Tianhe-2 supercomputer with 24 virtual CPUs and 88 GiB of memory. All combinations were configured to schedule tasks over all 24 virtual CPUs. The coverages of the down-sampled datasets were approximately 20X, 40X, 60X, 80X, 100X, respectively. Among them, variants calling in SK2 sets 24 threads, GATK used the default setting thread in BQSR and 24 threads setting in variants calling, and SV used the default setting thread in mpileup and variants calling.