> 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.md). # Annotation Engine ## 4.0 - 30 September 2026 These release notes include new features, product limitations, and known issues for DRAGEN Annotation Engine 4.0. For prior release notes, see [Annotation Engine previous releases](/annotation/release-notes/annotation-engine/annotation-engine-previous-releases.md). #### New Features * New command line interface * Print error message for corrupt SA files * Multi-worker annotator * Output all VCF info and sample fields in JSON * Consistent Annotation across VCF representation * ISCN parental notation #### Resolved Issues * Fixed single base deletions at intron reported as frame\_shift * Fixed crashing on HGVS computation * Updated Variant Frequency calculation * Fixed blank VCF line causing crash * Annotator now skips VCF lines with REF==ALT instead of crashing * Fixed duplicate gene entries in gene section * Fixed VCF Info parsing error on . value * Fixed error parsing VCF info field FLAG type without description in header * Fixed amino acid count argument out of range #### 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 | --- # 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. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation by asking a question. Perform an HTTP GET request on the following URL with the `ask` and `goal` query parameters: ``` GET https://help.bioinsight.illumina.com/annotation/release-notes/annotation-engine.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is what the user is ultimately trying to achieve, the reason they need the answer. Sharing it helps GitBook give you a better, more relevant answer. A goal is most helpful when it describes the outcome the user wants rather than restating the question. For example, with `ask=how do I create an API token`, a goal like `automate deployments from our CI pipeline` lets GitBook tailor the answer to that use case. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.