> For the complete documentation index, see [llms.txt](https://docs.omics.ai/products/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.omics.ai/products/workbench/variant-interpreter.md).

# Variant Interpreter

The Variant Interpreter is an interactive workspace for reviewing the variants called from a sample's long-read genome and producing a clinical report. It takes the output of a completed tertiary analysis workflow and presents it as a single, navigable case covering small variants, structural variants, copy-number variants, tandem repeats, and paralogs, so that a clinical geneticist can move from raw calls to a submitted interpretation in one sitting.

## Who this is for

Everyone who works on a case does so through a workspace **role** that controls what they can do. There are three — see [Workspaces & roles](/products/workbench/variant-interpreter/workspaces-and-roles.md) for the full capability matrix:

* **Contributor** — the day-to-day interpreter, typically a clinical geneticist or analyst: reviews prioritized candidate variants, evaluates evidence, classifies variants, and drafts the report.
* **Admin** — everything a Contributor can do, plus report **sign-off** (typically the lab director), the lab's report templates and branding, and workspace administration.
* **Viewer** — read-only access, for anyone who needs to follow a case without changing it.

## Where it fits

The Variant Interpreter is the final, tertiary stage of analysis. It sits downstream of:

1. **Secondary analysis**: the long-read WGS workflow (run in [Workbench](/products/workbench/introduction.md)) that aligns reads and calls variants. This produces phased VCFs, structural and copy-number calls, tandem repeat genotypes, and methylation pileups.
2. **Annotation & filtering**: population-frequency annotation and candidate filtering that reduce millions of raw calls to a reviewable shortlist.

The Variant Interpreter then loads that prepared case so the CG can interpret it. For the exact tools and versions behind a given case, see [Pipeline & caller versions](/products/workbench/variant-interpreter/pipeline-and-caller-versions.md).

{% hint style="info" %}
The Variant Interpreter does not call variants itself. What you review here reflects the workflow version that produced the case; the sample drawer records which workflow and caller versions were used.
{% endhint %}

## What you can do

* Find a sample and open its analysis from the [Data Page](/products/workbench/variant-interpreter/getting-started/the-data-page.md).
* Orient on the [Summary tab](/products/workbench/variant-interpreter/getting-started/the-summary-tab.md) and triage the priority findings.
* Review [small variants](/products/workbench/variant-interpreter/reviewing-variants/small-variants.md), [structural variants](/products/workbench/variant-interpreter/reviewing-variants/structural-variants.md), [copy number](/products/workbench/variant-interpreter/reviewing-variants/copy-number.md), [tandem repeats](/products/workbench/variant-interpreter/reviewing-variants/tandem-repeats.md), [paralogs](/products/workbench/variant-interpreter/reviewing-variants/paralogs.md), and [methylation](/products/workbench/variant-interpreter/reviewing-variants/methylation-imprinting.md).
* Check whether two variants in a gene are [in cis or in trans](/products/workbench/variant-interpreter/reviewing-variants/haplotype-phase.md).
* [Search](/products/workbench/variant-interpreter/reviewing-variants/search.md) for variants in specific genes across every variant type.
* Apply lab and case-level [filters](/products/workbench/variant-interpreter/filtering-and-prioritization.md).
* [Classify](/products/workbench/variant-interpreter/classifying-variants.md) variants and add them to the report.
* [Fill in the report](/products/workbench/variant-interpreter/generating-a-report/filling-in-a-report.md) from your lab's [report templates](/products/workbench/variant-interpreter/generating-a-report/report-templates.md), then [sign off and release it](/products/workbench/variant-interpreter/generating-a-report/sign-off-and-release.md).


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