Tuesday, May 6, 2014

Fwd: Jannovar: A Java Library for Exome Annotation

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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.

Thumbnail image of graphical abstract

Jannovar is a Java library for annotating VCF files from exome and genome sequences that uses an interval tree for rapid and accurate identification of affected transcripts. Jannovar generates HGVS-compliant annotations for a wide range of variant classes and additionally can be used for pedigree analysis.

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(Via human mutation.)