Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, 1090 Vienna, Austria.
Fondazione Istituto Italiano di Tecnologia, 16163 Genoa, Italy.
Nucleic Acids Res. 2017 Jul 3;45(W1):W567-W572. doi: 10.1093/nar/gkx425.
Next generation sequencing is widely used to link genetic variants to diseases, and it has massively accelerated the diagnosis and characterization of rare genetic diseases. After initial bioinformatic data processing, the interactive analysis of genome, exome, and panel sequencing data typically starts from lists of genetic variants in VCF format. Medical geneticists filter and annotate these lists to identify variants that may be relevant for the disease under investigation, or to select variants that are reported in a clinical diagnostics setting. We developed VCF.Filter to facilitate the search for disease-linked variants, providing a standalone Java program with a user-friendly interface for interactive variant filtering and annotation. VCF.Filter allows the user to define a broad range of filtering criteria through a graphical interface. Common workflows such as trio analysis and cohort-based filtering are pre-configured, and more complex analyses can be performed using VCF.Filter's support for custom annotations and filtering criteria. All filtering is documented in the results file, thus providing traceability of the interactive variant prioritization. VCF.Filter is an open source tool that is freely and openly available at http://vcffilter.rarediseases.at.
下一代测序技术被广泛用于将遗传变异与疾病联系起来，它极大地加速了罕见遗传病的诊断和特征描述。在进行初步的生物信息学数据处理后，基因组、外显子组和面板测序数据的交互式分析通常从 VCF 格式的遗传变异列表开始。医学遗传学家筛选和注释这些列表，以识别可能与正在研究的疾病相关的变异，或选择在临床诊断环境中报告的变异。我们开发了 VCF.Filter 来方便寻找与疾病相关的变异，提供了一个带有用户友好界面的独立 Java 程序，用于交互式变异筛选和注释。VCF.Filter 允许用户通过图形界面定义广泛的筛选标准。常见的工作流程，如 trio 分析和基于队列的筛选，都已预先配置，而更复杂的分析可以使用 VCF.Filter 对自定义注释和筛选标准的支持来执行。所有筛选都记录在结果文件中，从而提供了交互式变异优先级排序的可追溯性。VCF.Filter 是一个开源工具，可在 http://vcffilter.rarediseases.at 免费公开获取。
