In this work, we extend vcfdist to be the first variant call benchmarking tool to jointly evaluate phased single-nucleotide polymorphisms (SNPs), small insertions/deletions (INDELs), and structural variants (SVs) for the whole genome. First, we find that a joint evaluation of small and structural variants uniformly reduces measured errors for SNPs (− 28.9%), INDELs (− 19.3%), and SVs (− 52.4%) across three datasets. vcfdist also corrects a common flaw in phasing evaluations, reducing measured flip errors by over 50%. Lastly, we show that vcfdist is more accurate than previously published works and on par with the newest approaches while providing improved result interpretability.

中文翻译：

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与 vcfdist 联合对小型和结构变体调用进行基准测试


在这项工作中，我们将 vcfdist 扩展为第一个变异调用基准测试工具，用于联合评估全基因组的定相单核苷酸多态性 (SNP)、小插入/缺失 (INDEL) 和结构变异 (SV)。首先，我们发现对小变异和结构变异的联合评估均匀地减少了三个数据集中的 SNP (− 28.9%)、INDEL (− 19.3%) 和 SV (− 52.4%) 的测量误差。 vcfdist 还纠正了定相评估中的一个常见缺陷，将测量的翻转误差减少了 50% 以上。最后，我们表明 vcfdist 比以前发表的作品更准确，并且与最新方法相当，同时提供了改进的结果可解释性。