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 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) 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:
Secondary analysis: the long-read WGS workflow (run in Workbench) that aligns reads and calls variants. This produces phased VCFs, structural and copy-number calls, tandem repeat genotypes, and methylation pileups.
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.
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.
What you can do
Find a sample and open its analysis from the Data Page.
Orient on the Summary tab and triage the priority findings.
Review small variants, structural variants, copy number, tandem repeats, and paralogs.
Apply lab and case-level filters.
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