使用变体工具对下一代测序研究中的遗传变异进行综合注释和分析。
Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant tools.
机构信息
Department of Epidemiology, University of Texas, MD Anderson Cancer Center, Houston, TX, USA.
出版信息
Bioinformatics. 2012 Feb 1;28(3):421-2. doi: 10.1093/bioinformatics/btr667. Epub 2011 Dec 2.
MOTIVATION
Storing, annotating and analyzing variants from next-generation sequencing projects can be difficult due to the availability of a wide array of data formats, tools and annotation sources, as well as the sheer size of the data files. Useful tools, including the GATK, ANNOVAR and BEDTools can be integrated into custom pipelines for annotating and analyzing sequence variants. However, building flexible pipelines that support the tracking of variants alongside their samples, while enabling updated annotation and reanalyses, is not a simple task.
RESULTS
We have developed variant tools, a flexible annotation and analysis toolset that greatly simplifies the storage, annotation and filtering of variants and the analysis of the underlying samples. variant tools can be used to manage and analyze genetic variants obtained from sequence alignments, and the command-line driven toolset could be used as a foundation for building more sophisticated analytical methods.
AVAILABILITY AND IMPLEMENTATION
variant tools consists of two command-line driven programs vtools and vtools_report. It is freely available at http://varianttools.sourceforge.net, distributed under a GPL license.
CONTACT
动机
由于存在各种数据格式、工具和注释来源，以及数据文件的庞大数量，存储、注释和分析下一代测序项目中的变体可能会很困难。有用的工具，包括 GATK、ANNOVAR 和 BEDTools，可以集成到自定义管道中，用于注释和分析序列变体。然而，构建支持跟踪变体及其样本的灵活管道，同时支持更新的注释和重新分析，并不是一项简单的任务。
结果
我们开发了变体工具，这是一个灵活的注释和分析工具集，极大地简化了变体的存储、注释和过滤以及底层样本的分析。变体工具可用于管理和分析从序列比对中获得的遗传变体，并且命令行驱动的工具集可以用作构建更复杂的分析方法的基础。
可用性和实现
变体工具由两个命令行驱动的程序 vtools 和 vtools_report 组成。它可在 http://varianttools.sourceforge.net 上免费获得，根据 GPL 许可证分发。
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