Large genotyping datasets have become commonplace due to efficient, cheap methods for SNP identification. Typical genotyping datasets may have thousands to millions of data points per accession, across tens to thousands of accessions. There is a need for tools to help rapidly explore such datasets, to assess characteristics such as overall differences between accessions and regional anomalies across the genome. We present GCViT (Genotype Comparison Visualization Tool), for visualizing and exploring large genotyping datasets. GCViT can be used to identify introgressions, conserved or divergent genomic regions, pedigrees, and other features for more detailed exploration. The program can be used online or as a local instance for whole genome visualization of resequencing or SNP array data. The program performs comparisons of variants among user-selected accessions to identify allele differences and similarities between accessions and a user-selected reference, providing visualizations through histogram, heatmap, or haplotype views. The resulting analyses and images can be exported in various formats. GCViT provides methods for interactively visualizing SNP data on a whole genome scale, and can produce publication-ready figures. It can be used in online or local installations. GCViT enables users to confirm or identify genomics regions of interest associated with particular traits. GCViT is freely available at https://github.com/LegumeFederation/gcvit . The 1.0 version described here is available at https://doi.org/10.5281/zenodo.4008713 .

中文翻译：

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GCViT：一种重新测序和 SNP 阵列数据的交互式全基因组可视化方法

由于高效、廉价的 SNP 鉴定方法，大型基因分型数据集已变得司空见惯。典型的基因分型数据集可能具有数千到数百万个数据点，跨越数万到数千个种质。需要工具来帮助快速探索此类数据集，以评估特征，例如种质之间的总体差异和整个基因组的区域异常。我们提出了 GCViT（基因型比较可视化工具），用于可视化和探索大型基因分型数据集。GCViT 可用于识别基因渗入、保守或不同的基因组区域、谱系和其他特征，以进行更详细的探索。该程序可以在线使用，也可以作为本地实例用于重测序或 SNP 阵列数据的全基因组可视化。该程序对用户选择的种质之间的变体进行比较，以识别种质与用户选择的参考之间的等位基因差异和相似性，通过直方图、热图或单倍型视图提供可视化。生成的分析和图像可以以各种格式导出。GCViT 提供了在全基因组规模上交互式可视化 SNP 数据的方法，并且可以生成可供发表的图形。它可用于在线或本地安装。GCViT 使用户能够确认或识别与特定性状相关的感兴趣的基因组学区域。GCViT 可在 https://github.com/LegumeFederation/gcvit 免费获得。此处描述的 1.0 版本可在 https://doi.org/10.5281/zenodo.4008713 获得。