Illumina Connected Annotations
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.
Credentials
Credentials are stored in a credentials JSON file. It will contain an Illumina API key to access Illumina platform. To access premium data sources, there are two options
DRAGEN server users will use DRAGEN serial number
DRAGEN cloud users will use their BYOL username and password
Illumina API Key
To generate an Illumina API key, create an Illumina account via https://accounts.login.illumina.com. Refer to this guide for instructions on obtaining your MyIlluminaApiKey.
Premium Sources
DRAGEN Server Users
To access premium sources, retrieve the DRAGEN serial number using the following command:
If you have multiple versions of DRAGEN installed, you have to execute the following command to get the versions
And then using the selected DRAGEN_VERSION execute the following to find the serial number
Finally, copy the serial number and create a credentials.json file as follows:
DRAGEN Cloud users
The serial number will not work for DRAGEN cloud users. Instead, the BYOL username and password needs to be used. Following template can be used to create the credentials.json.
Please follow the guide here for more detail information to create the credential file including how to create Illumina account and generating MyIlluminaApiKey.
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 assemblyFile
all_annotations_GRCh38.json: configurations for producing full variant annotation (running Dragen with parameter --enable-variant-annotation true) for GRCh38 assemblyFile
germline_tagging_annotations_GRCh37.json: configurations required when running Dragen pipeline that perform germline tagging step for GRCh37 assemblyFile
germline_tagging_annotations_GRCh38.json: configurations required when running Dragen pipeline that perform germline tagging step for GRCh38 assemblyFile
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 ingermline_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 ingermline_tagging_annotations_GRCh38.json)
To download, execute the command below for each of the JSON file defined above:
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 forgermline_tagging_annotations_[assembly].json.Data defined in
tmb_annotations_[assembly].jsonare needed if Dragen is run with--enable-tmb trueparameter. Without data defined intmb_annotations_[assembly].jsonavailable, running Dragen will result in error.Data defined in
germline_tagging_annotations_[assembly].jsonare needed if Dragen is run with--vc-enable-germline-tagging trueparameter. Without data defined intmb_annotations_[assembly].jsonavailable, running Dragen will result in error.
For complete guide on how to use DataManager, please read this guide here.
Below is the output example when running the DataManager to download using all_annotations_GRCh38.json config file:
Annotate Files (via DRAGEN command-line)
To automatically annotate output VCFs, please add the following command-line arguments:
--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. To annotate hg19 variants, please use GRCh37
--annotation-data-config
/path/to/resources/annotation/all_annotations_GRCh38.json
path to data config file used for data downloading (same as --versions-config)
All the command-line arguments shown together:
Annotate Files (via standalone Illumina Connected Annotations)
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:
The following are the available command line options:
-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.
JSON Output File
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. Newer versions of Annotations are backward compatible, and can therefore annotate output files from older DRAGEN releases.
3.6, 3.7
3.9.0
spliceAI, primateAI
Not Available
Not Available
3.5
3.6.0
spliceAI, primateAI
Not Available
Not Available
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