Dong Ruining, Cameron Daniel, Bedo Justin, Papenfuss Anthony T
Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia.
Department of Medical Biology, University of Melbourne, VIC 3010, Australia.
GigaByte. 2022 Oct 5;2022:gigabyte70. doi: 10.46471/gigabyte.70. eCollection 2022.
Nuclear integration of mitochondrial genomes and retrocopied transcript insertion are biologically important but often-overlooked aspects of structural variant (SV) annotation. While tools for their detection exist, these typically rely on reanalysis of primary data using specialised detectors rather than leveraging calls from general purpose structural variant callers. Such reanalysis potentially leads to additional computational expense and does not take advantage of advances in general purpose structural variant calling. Here, we present svaRetro and svaNUMT; R packages that provide functions for annotating novel genomic events, such as nonreference retrocopied transcripts and nuclear integration of mitochondrial DNA. The packages were developed to work within the Bioconductor framework. We evaluate the performance of these packages to detect events using simulations and public benchmarking datasets, and annotate processed transcripts in a public structural variant database. svaRetro and svaNUMT provide modular, SV-caller agnostic tools for downstream annotation of structural variant calls.
线粒体基因组的核整合和反转录拷贝插入是结构变异（SV）注释中生物学上重要但常被忽视的方面。虽然存在用于检测它们的工具，但这些工具通常依赖于使用专门的检测器对原始数据进行重新分析，而不是利用通用结构变异调用程序的调用结果。这种重新分析可能会导致额外的计算成本，并且无法利用通用结构变异调用方面的进展。在这里，我们展示了svaRetro和svaNUMT；R包，它们提供了用于注释新的基因组事件的功能，例如非参考反转录拷贝转录本和线粒体DNA的核整合。这些包是为在Bioconductor框架内工作而开发的。我们使用模拟和公共基准数据集评估这些包检测事件的性能，并在公共结构变异数据库中注释处理后的转录本。svaRetro和svaNUMT为结构变异调用的下游注释提供了模块化的、与SV调用程序无关的工具。
