Illumina Connected Annotations, also known as Illumina Annotation Engine (IAE) or Nirvana provides translational research-grade annotation of genomic variants (SNVs, MNVs, insertions, deletions, indels, STRs, gene fusions, and SVs (including CNVs). It can be run as a stand-alone package, or integrated into larger software tools that require variant annotation.
Users can annotate VCF files by enabling annotation on the DRAGEN command-line or by running the standalone tool.
The input to Illumina Connected Annotations are VCFs and the output is a structured JSON representation of all annotation and sample information (as extracted from the VCF). Illumina Connected Annotations handles multiple alternate alleles and multiple samples with ease.
NOTE: Before running Annotations, the external data sources, gene models, and reference genome needs to be downloaded from our annotation server.
By default, the Annotations binaries are located in the /opt/dragen/<VERSION>/share/nirvana directory. This directory includes two files: the Downloader and Nirvana (Illumina Connected Annotations).
Limitations
Illumina Connected Annotations and the Downloader are compatible with the following platforms:
CentOS 7, Oracle 8 and other modern Linux distributions using x64 processors.
NOTE: If the DRAGEN server does not have an internet connection, the Downloader executable can be copied to a non-DRAGEN server that is connected to the internet to download the annotation data. Once the download has completed, the annotation data can then be copied locally to the DRAGEN server for subsequent annotation.
Annotate Files (via DRAGEN command-line)
To automatically annotate output VCFs, please add the following command-line arguments:
Argument
Example
Description
--enable-variant-annotation
true
enables annotation if the pipeline supports it
--variant-annotation-data
/path/to/your/NirvanaData
the location where you downloaded the Nirvana annotation files
--variant-annotation-assembly
GRCh38
the genome assembly - either GRCh37 or GRCh38. hg19 is handled properly by using GRCh37
Annotations produces an output file in JSON format. Please refer to Illumina Connected Annotations JSON for detailed description of the JSON file.
Version History
Annotations binaries have been included with DRAGEN since v3.5. The table below indicates which version of Annotations binaries were included with different DRAGEN releases, and their AI annotation capabilities.
The Annotations binaries distributed with DRAGEN can not be changed. Never versions of Annotations are backward compatible, and can therefore annotate output files from older DRAGEN releases.