Jäger Marten, Wang Kai, Bauer Sebastian, Smedley Damian, Krawitz Peter, Robinson Peter N
Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany; Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Berlin, Germany.
Hum Mutat. 2014 May;35(5):548-55. doi: 10.1002/humu.22531. Epub 2014 Apr 9.
Transcript-based annotation and pedigree analysis are two basic steps in the computational analysis of whole-exome sequencing experiments in genetic diagnostics and disease-gene discovery projects. Here, we present Jannovar, a stand-alone Java application as well as a Java library designed to be used in larger software frameworks for exome and genome analysis. Jannovar uses an interval tree to identify all transcripts affected by a given variant, and provides Human Genome Variation Society-compliant annotations both for variants affecting coding sequences and splice junctions as well as untranslated regions and noncoding RNA transcripts. Jannovar can also perform family-based pedigree analysis with Variant Call Format (VCF) files with data from members of a family segregating a Mendelian disorder. Using a desktop computer, Jannovar requires a few seconds to annotate a typical VCF file with exome data. Jannovar is freely available under the BSD2 license. Source code as well as the Java application and library file can be downloaded from http://compbio.charite.de (with tutorial) and https://github.com/charite/jannovar.
基于转录本的注释和系谱分析是遗传诊断和疾病基因发现项目中全外显子组测序实验计算分析的两个基本步骤。在此，我们展示了Jannovar，一个独立的Java应用程序以及一个Java库，旨在用于更大的外显子组和基因组分析软件框架。Jannovar使用区间树来识别受给定变异影响的所有转录本，并为影响编码序列、剪接位点以及非翻译区和非编码RNA转录本的变异提供符合人类基因组变异协会标准的注释。Jannovar还可以使用包含分离孟德尔疾病的家庭成员数据的变异调用格式（VCF）文件进行基于家系的系谱分析。使用台式计算机，Jannovar需要几秒钟来注释一个包含外显子组数据的典型VCF文件。Jannovar在BSD2许可下可免费获取。源代码以及Java应用程序和库文件可从http://compbio.charite.de（附带教程）和https://github.com/charite/jannovar下载。
