SMASH: a benchmarking toolkit for human genome variant calling
SMASH: a benchmarking toolkit for human genome variant calling
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DOI：
10.1093/bioinformatics/btu345
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发表时间：
2014-10-01
期刊：
影响因子：
5.8
通讯作者：
Patterson, David
中科院分区：
文献类型：
--
作者：
Talwalkar, Ameet;Liptrap, Jesse;Patterson, David
动机：计算方法对于从原始测序数据中提取可操作的信息至关重要，从而实现下一代测序技术的承诺。不幸的是，为从人类测序数据中调用变体而开发的计算工具在许多预测上存在分歧，而且当前评估准确性和计算性能的方法是临时且不完整的。协议的基准变异调用方法将刺激基因组处理工具的发展，促进researchers.Results之间的沟通：我们提出SMASH，一个基准方法评估生殖系变异调用算法。我们生成合成数据集，组织和解释广泛的现有基准测试数据的真实的基因组，并提出了一套准确性和计算性能的指标，这些基准测试数据的变异调用方法进行评估。此外，我们说明了实用的SMASH来评估一些领先的单核苷酸多态性，插入缺失和结构变异调用算法的性能。
Motivation: Computational methods are essential to extract actionable information from raw sequencing data, and to thus fulfill the promise of next-generation sequencing technology. Unfortunately, computational tools developed to call variants from human sequencing data disagree on many of their predictions, and current methods to evaluate accuracy and computational performance are ad hoc and incomplete. Agreement on benchmarking variant calling methods would stimulate development of genomic processing tools and facilitate communication among researchers.Results: We propose SMASH, a benchmarking methodology for evaluating germline variant calling algorithms. We generate synthetic datasets, organize and interpret a wide range of existing benchmarking data for real genomes and propose a set of accuracy and computational performance metrics for evaluating variant calling methods on these benchmarking data. Moreover, we illustrate the utility of SMASH to evaluate the performance of some leading single-nucleotide polymorphism, indel and structural variant calling algorithms.