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Version: 3.24 (unreleased)

Licensed Content

Illumina Conncted Annotations supports following content which is available through a license from Illumina. The license file will allow users to download and annotate with these data sources.

  • COSMIC
  • OMIM
  • Primate AI-3D
  • Splice AI
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License may be customized to allow access to one of more of the above at the time of license creation.

note

The Annotator packaged with DRAGEN comes with a license for all premium contents. That is, if the Annotator is run from within DRAGEN, all premium content will be available. However, this doesn't automatically grant a license to get premium contents while running the Annotator outside of DRAGEN. You may use your DRAGEN box serial number to access licensed content (see below).

How to obtain the license?

There are two ways of obtaining a license:

  1. Please contact annotation_support@illumina.com to obtain a special credentials file for the data sources of interest.
  2. If you are a DRAGEN user, you may use your DRAGEN serial number directly.

Visit Illumina Connected Annotations for more details.

How to use the credentials file?

After obtaining the credentials file, it may be used in two ways:

  1. Home folder
  2. Commandline argument

The default location of the license file is ~/.ilmnAnnotations/credentials.json but this file may be saved at any location and passed in as commandline argument.

  1. File with special credentials:
{
  "MyIlluminaApiKey": "<your Illumina account api key>",
  "ApiKey": "<your professional data source API key>",
  "ApiSecret": "<your professional data source API secret>"
}
  1. File with DRAGEN serial number:
{
  "MyIlluminaApiKey": "<your Illumina account api key>",
  "DragenSerialNo": "<your DRAGEN box serial number>"
}

Autogenerated Licence file

The DataManager will also download a file that will be stored alongside the path of credentials.json file, named premium.lic. This file contains the encoded information for accessing the licensed content. It is automatically managed and used by Annotator and Data Manager, and user intervention is not needed.

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If you are experiencing licensing errors, you can delete this file. Running Annotator or Data Manager will automatically fetch a new premium.lic file based on your allowed professional content.

Offline Mode

It should be noted that professional content is protected through online license verification system which works in the background. If you intend to run Annotator without internet access, make sure the premium.lic (which was auto downloaded by Data Manager) is present alongside the credentials.json file. The autogenerated file: premium.lic will expire after 90 days and must be re-downloaded from internet.

Re-downloading premium.lic

The file premium.lic will be automatically downloaded once Data Manager is used to re-download any sources. Running Annotator with internet access will also re-download this file. Once this file is re-downloaded, it may be used for offline use for another 90 days.

Download licensed content

See: DataManager Make sure to include the credentials.json file

Annotate with licensed content

Make sure to include the credentials.json file

dotnet Annotator.dll \
--ref ~/data/References/7/Homo_sapiens.GRCh38.Nirvana.dat \
--sd ~/data/SupplementaryDatabase/GRCh38 \
-c ~/data/Cache/32 \
-i ~/input_vcf-hg38.vcf.gz \
-o ~/output \
--credentials-file ~/credentials.json

Licensing Errors

If the license has expired, Illumina Connected Annotations will stop annotating and exit with an error code. These errors may be skipped by using the --ignoreLicenseError command line argument. After doing this, only basic data sources will be used for annotations. This can also be achieved by deleting the credentials file from the home folder.