title: Jannovar: a java library for exome annotation.
abstract: 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.
authors.affiliation: Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany; Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Berlin, Germany.
authors.forename: Marten
authors.initials: M
authors.lastname: Jäger
authors.forename: Kai
authors.initials: K
authors.lastname: Wang
authors.forename: Sebastian
authors.initials: S
authors.lastname: Bauer
authors.forename: Damian
authors.initials: D
authors.lastname: Smedley
authors.forename: Peter
authors.initials: P
authors.lastname: Krawitz
authors.forename: Peter N
authors.initials: PN
authors.lastname: Robinson
mesh_terms: D019295:Computational Biology; D059472:Exome / Q000235:genetics*; D015894:Genome, Human; D006801:Humans; D058977:Molecular Sequence Annotation; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
keywords: bioinformatics; exome sequencing; genomic annotation; interval tree