Jannovar as a Library

You can obtain the Jannovar library JAR files from Maven Central. Pre-built binaries are available from Maven Central. This query yields the Jannovar libraries.

Note

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.

API Documentation

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 jannovar-htsjdk.

<dependency>
        <groupId>de.charite.compbio</groupId>
        <artifactId>jannovar-htsjdk</artifactId>
        <version>0.35-SNAPSHOT</version>
</dependency>

Otherwise, there are the following JAR files:

jannovar-cli
Command line interface for Jannovar, not a library.
jannovar-core
Core Jannovar functionality with molecular impact annotation and inheritance filtering.
jannovar-hgvs
Support for parsing HGVS Variant Nomenclature and representing HGVS variants as Java objects.
jannovar-htsjdk
Bridge between core Jannovar functionality and HTSJDK
jannovar-inheritance-checker
Older version of inheritance filtering.
jannovar-vardbs
Support for annotating variants with VCF databases from various sources, e.g. dbSNP