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 either a structured JSON representation of all annotation and sample information (as extracted from the VCF) or an annotated VCF. Please note that the annotated VCF only contains a subset of the annotations provided in the JSON output. This tool can handle multi-sample VCFs.
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 <INSTALL_PATH>/share/nirvana directory. This directory includes two files: Nirvana (Illumina Connected Annotations) and DataManager.
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.
Downloading Annotation Data Files
Variant annotation in Dragen requires additional annotation data files that have to be downloaded prior to running any Dragen pipeline that requires variant annotation. To download, please use the DataManager software that is located in <INSTALL_PATH>/share/nirvana/DataManager. To be able to download data successfully, a credential file has to be created.
A credential file will contain an Illumina API key and a premium data source license that you have obtained. To generate Illumina API key, You have to create an Illumina account via this . As for the premium data license, you can use your existing license key and secret if you already have one or your Dragen serial number. You can use this command to get your Dragen serial number:
dragen_info -b | grep Serial
An example of credential file with Dragen serial number information:
{
"MyIlluminaApiKey": "<your Illumina account api key>",
"DragenSerialNo": "<your Dragen server serial no.>"
}
Once the credential file is created with your Illumina API key and your premium data license information, you can start to download those files. Dragen has a predefined set of files that has to be downloaded. The configurations are in Dragen resources directory <INSTALL_PATH>/resources/annotation. There are several JSON config files in the directory:
File all_annotations_GRCh37.json : configurations for producing full variant annotation (running Dragen with parameter --enable-variant-annotation true) for GRCh37 assembly
File all_annotations_GRCh38.json : configurations for producing full variant annotation (running Dragen with parameter --enable-variant-annotation true) for GRCh38 assembly
File germline_tagging_annotations_GRCh37.json : configurations required when running Dragen pipeline that perform germline tagging step for GRCh37 assembly
File germline_tagging_annotations_GRCh38.json : configurations required when running Dragen pipeline that perform germline tagging step for GRCh38 assembly
File tmb_annotations_GRCh37.json : configurations required when running Dragen pipeline that perform TMB step for GRCh37 assembly (this file will also contain all data that are defined in germline_tagging_annotations_GRCh37.json)
File tmb_annotations_GRCh38.json : configurations required when running Dragen pipeline that perform TMB step for GRCh38 assembly (this file will also contain all data that are defined in germline_tagging_annotations_GRCh38.json)
To download, execute the command below for each of the JSON file defined above:
.<INSTALL_PATH>/share/nirvana/DataManager download -r [assembly] --credentials-file [path to credential file] --dir [path to directory for the downloaded data] --versions-config [path to the JSON file in the resources folder]
For the --dir argument you can use the same directory for all config file so that it is stored in the same directory. This directory path will be used for parameter --variant-annotation-data when running Dragen.
NOTE:
If you have run the DataManager for tmb_annotations_[assembly].json, you don't need to run it for germline_tagging_annotations_[assembly].json.
Data defined in tmb_annotations_[assembly].json are needed if Dragen is run with --enable-tmb true parameter. Without data defined in tmb_annotations_[assembly].json available, running Dragen will result in error.
Data defined in germline_tagging_annotations_[assembly].json are needed if Dragen is run with --vc-enable-germline-tagging true parameter. Without data defined in tmb_annotations_[assembly].json available, running Dragen will result in error.
Below is the output example when running the DataManager to download using all_annotations_GRCh38.json config file:
Please note that Illumina Connected Annotations supports uncompressed VCF files and bgzip compressed VCF files. VCF files that have been compressed by standard gzip are not supported.
To annotate the file, enter the following command:
<INSTALL_PATH>/share/nirvana/Nirvana -c [path to data dir]/Cache \
-r [path to data dir]/References/Homo_sapiens.GRCh38.Nirvana.dat \
--sd [path to data dir]/SupplementaryAnnotation/GRCh38 \
-l [path to credential file] --versions-config [path to resource directory]/all_annotations_GRCh38.json
-i <input_VCF> -o <output_prefix>
The following are the available command line options:
Option
Value
Example
Description
-c
directory
~/Data/Cache/
Cache directory
-r
directory
~/Data/References/Homo_sapiens.GRCh38.Nirvana.dat
Reference directory
--sd
directory
~/Data/SupplementaryAnnotation/GRCh38
Supplementary annotation directory
-i
path
<input_VCF>
Input VCF path
-o
prefix
<output_prefix>
Output path prefix
-l
file path
credentials.json
path to credential file
--versions-config
file path
all_annotations_GRCh38.json
path to versions config file
Using the example above, Annotations generates the following output.
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.
Newer versions of Annotations are backward compatible, and can therefore annotate output files from older DRAGEN releases.
DRAGEN version(s)
Annotations version
AI annotations
4.4
3.25
spliceAI, primateAI3D
4.3
3.23
spliceAI, primateAI3D
3.9, 3.10, 4.0, 4.1, 4.2
3.16.1
spliceAI, primateAI
3.8
3.14
spliceAI, primateAI
3.6, 3.7
3.9.0
spliceAI, primateAI
3.5
3.6.0
spliceAI, primateAI
Please follow the guide for more detail information to create the credential file including how to create Illumina account and generating MyIlluminaApiKey.
For complete guide on how to use DataManager, please read this guide .
Annotations produces an output file in JSON format. Please refer to for detailed description of the JSON file.
