短读对齐器在生殖系变种识别中的性能
Richard Wilton1, Alexander S Szalay1,2
1Department of Physics and Astronomy, Johns Hopkins University, Baltimore, MD 21218, United States.
Bioinformatics (Oxford, England)
|August 1, 2023
概括
优化DNA序列变异调用需要仔细选择短读对齐器和变异调用器. 这项研究将BWA-MEM,Bowtie 2和Arioc与DeepVariant,FreeBayes和GATK HaplotypeCaller一起评估,以提高生殖系变异调用精度.
科学领域:
- 基因组学就是基因组学.
- 生物信息学是一种生物信息学.
- 计算生物学 计算生物学
背景情况:
- 精确的DNA序列变异表征依赖于精确的读取对齐.
- 变量调用精度受到对齐器质量,调用软件及其相互作用的影响.
研究的目的:
- 评估短读对齐器性能,以优化生殖系变种调用精度.
- 分析对齐器配置和变量调用者行为之间的相互作用.
主要方法:
- 三种通用短读对齐器的性能评估:BWA-MEM,Bowtie 2和Arioc.
- 评估与三种生殖系变异调用者一起进行:DeepVariant,FreeBayes和GATK HaplotypeCaller.
- 对变量调用器关键数据元素的对齐器行为进行分析.
主要成果:
- 展示调整器和调用器的运行时配置如何影响变量调用性能.
- 确定影响生殖系变异调用精度的关键相互作用.
- 对调整器-调用器组合的比较分析.
结论:
- 读取对齐器和变体调用器的选择,以及它们的配置,对于准确的生殖系变体调用至关重要.
- 了解这些相互作用可以指导变量调用管道的优化.
- 对软件工具相互作用的进一步研究是有必要的,以推进基因组分析.
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