Jointly benchmarking small and structural variant calls with vcfdist

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2024-10-02 DOI:10.1186/s13059-024-03394-5

Tim Dunn, Justin M. Zook, James M. Holt, Satish Narayanasamy

引用次数: 0

Abstract

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.

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利用 vcfdist 对小变异和结构变异调用进行联合基准测试

在这项工作中，我们对 vcfdist 进行了扩展，使其成为首个联合评估全基因组分阶段单核苷酸多态性 (SNP)、小插入/缺失 (INDEL) 和结构变异 (SV) 的变异调用基准工具。首先，我们发现对小变异和结构变异进行联合评估可在三个数据集上一致地减少 SNP（- 28.9%）、INDEL（- 19.3%）和 SV（- 52.4%）的测量误差。最后，我们证明 vcfdist 比以前发表的作品更准确，与最新的方法不相上下，同时还提高了结果的可解释性。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

21.00

自引率

3.30%

发文量

241

审稿时长

2 months

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