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Welcome
Illumina Connected Annotations is a software tool that provides translational research-grade variant annotation from AI models and traditional sources for genomic data.
It annotates SNVs, MNVs, insertions, deletions, indels, STRs, gene fusions, and structural variants, including CNVs. You can run it as a standalone package or embed it in larger workflows.
Inputs are VCF files. Outputs are structured JSON or optional VCF. JSON is the default and most complete output format. VCF output supports a reduced annotation set.
Illumina Connected Annotations supports multi-allelic and multi-sample VCFs. It is developed under a rigorous software development lifecycle (SDLC) process with continuous validation against large baseline annotation sets.
Illumina Connected Annotations supports GRCh37.p13 and GRCh38.p14. We recommend using GRCh38.p14 for any new work. See specific versioned user guides for details on supported reference genomes.
Supplementary annotations
Illumina Connected Annotations adds external data sources for variant and gene context.
Content is available in two tiers:
Basic — available without a premium license
Professional — requires a license
For licensing details, see Licensed Content. For access, contact annotation_support@illumina.com.
