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

note

License may be customized to allow access to one of more of the above at the time of license creation.

How to obtain the license?

Please contact annotation_support@illumina.com to obtain a special credentials file for the data sources of interest.

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. An example of credentials file as below:

{
    "ApiKey":"myApiKey",
    "ApiSecret": "abcdefghikjlmnopqrstuvwxyz-secretKey"
}

However, this can be overridden by the command line argument while downloading/annotating.

Download licensed content

dotnet Downloader.dll \
-o ~/data \
-ga GRCh38 \
--credentialsFile ~/credentials.json

Annotate with licensed content

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