A Java API for high-throughput sequencing data (HTS) formats

ADAM_2.12: Core

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

Compression utility classes.

A library for manipulating bioinformatics sequencing formats in Apache Spark.

jannovar-htsjdk is the module for bridging between Jannovar and HTSJDK

Development on GATK 4

Conversions between HTSJDK and Big Data Genomics Avro Formats

jannovar-filter helps with applying threshold-based filters for WES/WGS filters

jannovar-stats helps in aggregating statistics about variants and variant annotations

jannovar-vardbs helps with using variant annotation databases, e.g. dbSNP