About Illumina Connected Annotations
Translational research-grade variant annotation
Illumina Connected Annotations 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.
Start here
Set up the standalone package in Getting Started with local download
Use the DRAGEN workflow in Getting Started with DRAGEN
Review Licensed Content for premium sources
What does Illumina Connected Annotations annotate?
Illumina Connected Annotations uses Sequence Ontology consequences to describe transcript impact.
Reference genome support
Illumina Connected Annotations supports GRCh37.p13 and GRCh38.p14.
Review the
GRCh37.p13chromosome and contig list in the assembly reportReview the
GRCh38.p14chromosome and contig list in the assembly report
Use GRCh38.p14 for new work.
Earlier GRCh38 releases had an alt-contig naming mismatch. This affected variant IDs and HGVS g. notation on some alt contigs. Main chromosomes were not affected.
Details on the earlier GRCh38 reference issue
Previous releases used GRCh38.p13 contig names from 109.20190607 with FASTA sequence from GRCh38.p12 109. This created mismatches for some alt contigs.
GRCh38.p14 fixes this issue and remains backward compatible with older transcript, gene model, and supplementary annotation files.
Transcript and gene models
Transcript consequences depend on the selected RefSeq or Ensembl release.
Illumina Connected Annotations uses gene models from RefSeq and Ensembl. The currently supported versions for GRCh38 are:
RefSeq
GCF_000001405.40-RS_2024_08
2024-08-26
RefSeq
GCF_000001405.40-RS_2023_10
2023-10-07
RefSeq
GCF_000001405.40-RS_2023_03
2023-03-21
Ensembl
113
2024-10-18
Ensembl
112
2024-05-14
Ensembl
110
2023-04-27
Ensembl
108
2022-10-20
For GRCh37:
RefSeq
105.20220307
2022-03-10
Ensembl
110
2023-02-08
Ensembl
108
2022-10-20
For GRCh37, Ensembl release 110 is effectively the same annotation set as release 87.
NCBI no longer publishes new GRCh37 RefSeq gene annotation releases. 105.20220307 is the final GRCh37 RefSeq release.
Gene symbols are sourced from HGNC as of 2024-06-03.
Use Data Manager to list supported versions and download them.
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.
Data management
Use Data Manager to:
list supported versions
download annotation files
validate local data
Download
Please visit Illumina Connected Annotations.
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