Jannovar as a Library¶
Note that you should only use JAR files from version 0.36 and not older versions. Some modules have been removed (and merged with other modules) in previous versions.
You can find the Jannovar Javadoc API documentation here:
Jannovar in your pom.xml¶
If you plan to process HTSJDK VariantContext objects then you will probably only need to depend on
<dependency> <groupId>de.charite.compbio</groupId> <artifactId>jannovar-htsjdk</artifactId> <version>0.36</version> </dependency>
Otherwise, there are the following JAR files:
- Command line interface for Jannovar, not a library.
- Core Jannovar functionality with molecular impact annotation and inheritance filtering.
- Support for parsing HGVS Variant Nomenclature and representing HGVS variants as Java objects.
- Bridge between core Jannovar functionality and HTSJDK
- Older version of inheritance filtering.
- Support for annotating variants with VCF databases from various sources, e.g. dbSNP