> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/annotation/release-notes/annotation-engine/annotation-engine-previous-releases.md). # Annotation Engine previous releases This page provide an archive of previous release notes. [Annotation Engine ](/annotation/release-notes/annotation-engine.md)provides the most current release notes. ## Annotation Engine 3.27 #### New Features · Consequence improvements · SV Annotation matching · Support annotating methylation · AlphaMissense Annotation · Consequence prioritization · ABraOM Supplementary Annotation · Support for single end BND · Updates to DataManager download · SV Consequence Improvements · Add DRAGEN licensing arguments support to Data Manager #### Resolved Issues · Fixed upstream/downstream gene variant hgvsc annotation does not consider transcript strand · Fixed lambda missing samples summary · Fixed case sensitivity when calling datasource names · Fixed NSI SV matcher ASCII input crash · Fixed Inframe\_deletion mislabeling #### Unresolved Issues · Single base deletion at intron is reported as frame\_shift · Annotations incorrectly determines gnomAD low complexity regions at translocation breakend boundaries · Annotations incorrectly handles insertions where RNA-edit insertions already occur #### Known Limitations | Issue ID | Summary | Remedy/Workaround | | -------- | ----------------------------------------------------------------------------------------------- | --------------------------------------------- | | NIR-919 | Annotations does not handle protein sequences that are partially aligned to the genome | No workaround. Fix planned for future version | | NIR-918 | Annotations does not handle ribosomal frameshifts properly during translation | No workaround. Fix planned for future version | | NIR-917 | Annotations does not truncate deletions that start within a deletion RNA-edit (HGVS c.) | No workaround. Fix planned for future version | | NIR-916 | Annotations does not detect HGVS c. duplications when inserting a base into a deletion RNA-edit | No workaround. Fix planned for future version | | NIR-915 | Annotations does not convert SNVs that land in a deletion RNA-edit as an insertion (HGVS c.) | No workaround. Fix planned for future version | ## Annotation Engine 3.25.1 #### New Features * Support for "." reference reads in PR/SR needed to support DUX4 caller * Enable --force-mt setting in Nirvana lambda * Make SVTYPE optional in VCF * Data Version Verification * DRAGEN License Check * Support for ISCN variant nomenclature standard * Up/down-stream HGVS * Downloader Service & Data Manager #### Resolved Issues * Handle cytoband for logical chromosome * Nirvana doesn't error out when no input param is set (--in or --vcf) * Nirvana show stack trace when input file doesn't exist * SA source selection not working * Jasix Null Exception While Indexing * Add user-friendly error message when user provides malformed tsv input * Jasix Null Exception While Indexing * Missing consequences when whole exons are deleted * Variant ID show N instead of using actual ref/alt allele * Invalid json format from clinvar phenotype field #### Unresolved Issues * Nirvana incorrectly determines gnomAD low complexity regions at translocation breakend\ boundaries * Nirvana incorrectly handles insertions where RNA-edit insertions already occur #### Known Limitations | Issue ID | Summary | Remedy/Workaround | | -------- | ----------------------------------------------------------------------------------------------- | --------------------------------------------- | | NIR-919 | Annotations does not handle protein sequences that are partially aligned to the genome | No workaround. Fix planned for future version | | NIR-918 | Annotations does not handle ribosomal frameshifts properly during translation | No workaround. Fix planned for future version | | NIR-917 | Annotations does not truncate deletions that start within a deletion RNA-edit (HGVS c.) | No workaround. Fix planned for future version | | NIR-916 | Annotations does not detect HGVS c. duplications when inserting a base into a deletion RNA-edit | No workaround. Fix planned for future version | | NIR-915 | Annotations does not convert SNVs that land in a deletion RNA-edit as an insertion (HGVS c.) | No workaround. Fix planned for future version | ## Annotation Engine 3.23 #### New features * Encrypted data format for paid supplementary annotation data sources * Pass ID field from VCF file to JSON * Added PhyloPPrimate to PhyloPPrimate supplementary annotation data sources * Implement license feature for paid supplementary data sources #### Updated features * Added qualitative classifications for PrimateAI-3D * Provided tiers for COSMIC Cancer Gene Census #### Data updates * Updated ClinGen DSM & GDV, OMIM, and ClinVar * Updated COSMIC to v99 #### Resolved issues * Omim downloader version path fix * Nirvana failing to annotate on alt contigs due to missing contig sequence in reference * Annotator always exits with 0 even with exception * Downloader in Prod uses manifest file from Dev #### Unresolved Issues * Nirvana incorrectly determines gnomAD low complexity regions at translocation breakend\ boundaries * Nirvana incorrectly handles insertions where RNA-edit insertions already occur #### Known Limitations | Issue ID | Summary | Remedy/Workaround | | -------- | ----------------------------------------------------------------------------------------------- | --------------------------------------------- | | NIR-919 | Annotations does not handle protein sequences that are partially aligned to the genome | No workaround. Fix planned for future version | | NIR-918 | Annotations does not handle ribosomal frameshifts properly during translation | No workaround. Fix planned for future version | | NIR-917 | Annotations does not truncate deletions that start within a deletion RNA-edit (HGVS c.) | No workaround. Fix planned for future version | | NIR-916 | Annotations does not detect HGVS c. duplications when inserting a base into a deletion RNA-edit | No workaround. Fix planned for future version | | NIR-915 | Annotations does not convert SNVs that land in a deletion RNA-edit as an insertion (HGVS c.) | No workaround. Fix planned for future version | ## Annotation Engine 3.22 #### New features * Add MANE select tag to transcripts * Consequence Impact #### Updated Features * PrimateAI-3D * Release Cache 32 * Update VF calculation on MT to reflect changes in DRAGEN variant calling * DRAGEN Somatic Caller MT VF Fix #### Data Updates * October 2023 data update (ClinGen DSM & GDV, OMIM, ClinVar, and dbSNP) #### Resolved Issues * Nirvana crashing at HGVS p. IsStartLost * NirvanaLambda failing to load Tabix index * Variant Rotator: prevent right shift for variants not in region * Nirvana Lambda: Tabix indexing is not moving the cursor to the beginning of the VCF line * Nirvana lambda returns a null in files list * Nirvana should simplify HGVS p. notation for deletions that disrupt the initiation codon * SingleAnnotation behaves differently in Lambda vs REST API #### Unresolved * Nirvana incorrectly determines gnomAD low complexity regions at translocation breakend\ boundaries * Nirvana incorrectly handles insertions where RNA-edit insertions already occur #### Known Limitations | Issue ID | Summary | Remedy/Workaround | | -------- | ----------------------------------------------------------------------------------------------- | --------------------------------------------- | | NIR-919 | Annotations does not handle protein sequences that are partially aligned to the genome | No workaround. Fix planned for future version | | NIR-918 | Annotations does not handle ribosomal frameshifts properly during translation | No workaround. Fix planned for future version | | NIR-917 | Annotations does not truncate deletions that start within a deletion RNA-edit (HGVS c.) | No workaround. Fix planned for future version | | NIR-916 | Annotations does not detect HGVS c. duplications when inserting a base into a deletion RNA-edit | No workaround. Fix planned for future version | | NIR-915 | Annotations does not convert SNVs that land in a deletion RNA-edit as an insertion (HGVS c.) | No workaround. Fix planned for future version | --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. 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