Case progress indicator (v100.40.0+)

Use the case progress indicator to determine where a case is in the analysis workflow and whether you need to take action.

The indicator appears in the Status column on the Cases page for cases with In progress, Re-Analysis, or Issue reported status.

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Case progress indicator meaning

This section explains what each progress indicator state means for cases with In progress or Re-Analysis status.

1. Secondary analysis running

Secondary analysis running

Indicator: Grey striped progress bar.

Meaning: The FASTQ‑based case is running DRAGEN secondary analysis.

2. Queued

Queued

Indicator: Empty segmented progress bar.

Meaning: The system has accepted the VCF (either a VCF case or the VCF output from integrated DRAGEN secondary analysis), but processing has not started yet.

3. Tertiary analysis running

Blue segments fill from left to right as the case moves through the five stages of the Emedgene tertiary analysis pipeline.

• A filled blue segment indicates a completed stage

• A half-filled blue segment indicates the stage in progress

Tooltip showing current stage, elapsed time, and estimated total processing time

Hover over the indicator to view:

• The current tertiary analysis stage

• Elapsed time since tertiary analysis started

• Estimated total processing time (when available).

3.1. Normalization

Normalization

Indicator: Segment 1 is half-filled.

Meaning: The system standardizes and prepares the uploaded data for downstream processing.

3.2. Annotation

Annotation

Indicator: Segment 1 is filled and segment 2 is half-filled.

Meaning: Variants are enriched with genomic, clinical, population, transcript, phenotype, and knowledge base annotations.

3.3. Indexing

Indexing

Indicator: Segments 1-2 are filled and segment 3 is half-filled.

Meaning: The annotated data is indexed to prepare the case for review within the platform.

3.4. Quality check

Quality check

Indicator: Segments 1-3 are filled and segment 4 is half-filled.

Meaning: The system performs quality validation.

3.5. AI Shortlist

AI Shortlist

Indicator: Segments 1-4 are filled and segment 5 is half-filled.

Meaning:

• The system performs AI-driven phenotype matching.

• The AI Shortlist performs variant prioritization, resulting in the list of Most Likely Candidates and Candidates for the case.

After all five tertiary analysis stages complete, the case status changes to Delivered.

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Case processing failure

In case of processing failure, Issue reported status may be supplemented with the progress indicator.

Secondary analysis failure

Secondary analysis failure

Indicator: Red striped progress bar.

Meaning: Failure during DRAGEN secondary analysis.

VCF file validation failure

Indicator: No progress indicator is shown.

Meaning: Input VCF file issues.

Tertiary analysis failure

Tertiary analysis failure at Quality check stage

Indicator: Progress bar shows completed tertiary analysis stages in blue and the failed stage in red.

Meaning: Processing stopped during the stage corresponding to the segment filled in red.

Hover over the indicator to confirm the failed stage. Select the question-mark icon () to view error details.

Tertiary analysis failure indicator

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Case status

Overview of case status behavior, history, and related workflows.

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Case statuses in a case lifecycle

Review status transitions, control types, and the reference status list.

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How to update a case status

Change the current case status from the case page or the Cases table.

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Case status management

Create custom statuses and reorder them for your organization.

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