Department of Bioinformatics, Genentech, South San Francisco, CA, USA.
23andMe, Mountain View, CA, USA.
Bioinformatics. 2017 Oct 15;33(20):3311-3313. doi: 10.1093/bioinformatics/btx450.
Variant calling is the complex task of separating real polymorphisms from errors. The appropriate strategy will depend on characteristics of the sample, the sequencing methodology and on the questions of interest.
We present VariantTools, an extensible framework for developing and testing variant callers. There are facilities for reproducibly tallying, filtering, flagging and annotating variants. The tools are extensible, modular and flexible, so that they are tunable to particular use cases, and they interoperate with existing analysis software so that they can be embedded in established work flows.
VariantTools is available from http://www.bioconductor.org/.
Supplementary data are available at Bioinformatics online.
变异调用是将真实多态性与错误区分开来的复杂任务。适当的策略将取决于样本的特征、测序方法以及感兴趣的问题。
我们提出了 VariantTools，这是一个用于开发和测试变异调用程序的可扩展框架。它具有可重复地计数、过滤、标记和注释变体的功能。这些工具具有可扩展性、模块化和灵活性，因此可以针对特定用例进行调整，并且可以与现有的分析软件互操作，以便可以将它们嵌入到既定的工作流程中。
VariantTools 可从 http://www.bioconductor.org/ 获取。
补充数据可在 Bioinformatics 在线获得。
