Jannovar as a Library¶
Note that you should only use JAR files from version 0.35-SNAPSHOT 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>0.35-SNAPSHOT</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