Computer Science and Engineering, University of Michigan, Ann Arbor, Michigan, USA.
National Institute of Standards and Technology, Gaithersburg, Maryland, USA.
Genome Biol. 2024 Oct 2;25(1):253. doi: 10.1186/s13059-024-03394-5.
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.
在这项工作中，我们将 vcfdist 扩展为第一个变体调用基准测试工具，以联合评估全基因组的相位单核苷酸多态性（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进行联合评估，可统一降低三个数据集上 SNP（-28.9%）、INDEL（-19.3%）和 SV（-52.4%）的测量误差。vcfdist 还纠正了相位评估中的一个常见缺陷，将测量的翻转错误减少了 50%以上。最后，我们表明，vcfdist 比以前的工作更准确，与最新的方法相当，同时提供了更好的结果可解释性。
