ABSTRACT
Jannovar is a stand-alone Java application as well as a Java library designed to be used in larger software frameworks for exome and genome analysis using the standardized Variant Call Format (VCF). The current version of Jannovar uses a compact variant of an interval tree to swiftly identify all transcripts affected by a given variant. Jannovar solves the basic problem of translating chromosomal coordinates to transcript variants. Variant calling programs usually generate chromosomal coordinates as reads are aligned to the reference while medical and biological interpretation usually require the prediction of the variant effects on individual transcripts and the corresponding proteins. Jannovar provides Human Genome Variation Society (HGVS)-compliant annotations both for variants affecting coding sequences and splice junctions as well as untranslated regions and noncoding RNA transcripts. This chapter explains how to download and install Jannovar and prepare for the analysis.
