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. 2021 Jul 20;10(7):giab048. doi: 10.1093/gigascience/giab048

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© The Author(s) 2021. Published by Oxford University Press GigaScience.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 1: — Low-coverage sequencing (LCS) study design. The flow chart summarizes the steps used to identify and impute polymorphic sites, where the green block represents the highly accurate pipeline used for Tn5-based LCS analysis (BaseVar-STITCH). We also generated SNP results using the GATK-Beagle pipeline (grey) and compared them with those obtained using the BaseVar-STITCH method. Three datasets (blue) were used to assess the accuracy of the results. The BaseVar-STITCH pipeline was used in the GWAS presented in this study. BWA: Burrows-Wheeler Aligner; HWE: Hardy-Weinberg equilibrium; QC: quality control.