The Workbench is the main view from a case, centralizing important information about the sample, the quality metrics and sometimes a short list of variants.
After uploading and processing completed, this page becomes the starting point for your evaluation.
On the top area, right by the case name, there are a few interesting options for a user regarding case management:
Top Left:
Sample Assay Information: Displays relevant data about the sample assay.
Case Assignee: Allows modification of the case assignee, selecting from a dropdown list of your organization's members.
Case Status: Indicates the current status of the case, which can be updated manually or automatically as the lab workflow progresses.
Top Right:
Export Options: Provides a dropdown menu for exporting various files, including VCF, FASTQ, or BAM (if available). You can also export Workbench results and other configurable case datasets.
The Workbench is divided into three main sections:
Case Details
The Case Details section displays all metadata from the case as uploaded into Franklin during its creation. You can modify this information, including phenotypic details, and apply virtual panels at the case level. For further details on virtual panels, please refer to the Virtual Panels article.
The Case Details section includes the following information:
Patient information: Sex, date of birth, ethnicity, family history, and physician comments.
Sample details: Ordering physician, specimen type, and collection and receiving dates.
Phenotypes: HPO terms selected from a dropdown list.
Case comments: Free-text comments or snippet choices entered by organization users, which appear in the case tile (my cases).
Panels: Both hard (view-only) and editable soft panels.
Family pedigree: Relevant for Family Cases.
Case and software version details.
By clicking on the "Edit" button on the top right, you can edit any of the details.
The case details section could be opened and edited in a dedicated tab as well:
Quality Control
The Workbench Quality Control section displays sample QC metrics. Choose the quality control tab to get the full display.
The complete QC metric list depends on the case type and the assay configuration, the QC metrics shown in this section may differ between organisations and assays.
When analyzing family cases, each member has a dedicated tab showing their sample's QC metrics, along with automatically calculated metrics like Consanguinity Check, Family Relationship Check, and UPD Check.
Franklin's bioinformatics team has set up default thresholds for the most common QC metrics. If a value is outside of the appropriate range, Franklin will show a warning sign in red. You can also place the cursor over the metric result to see a short explanation of each metric.
💡Franklin Professional can supports more than 50 out-of-the-box QC metrics, and most custom ones as well. We can adjust the thresholds to fit the pass/fail criteria for your specific organization.
Analysis Results
The Analysis Results section shows the variants that were selected by Franklin's AI-driven prioritization engine as clinically relevant for the case. This allows you to start your case analysis by reviewing the variants that are more likely to be causal for the conditions, to reach faster results.
Franklin's prioritization algorithms are complex, but in essence, they take into account:
The variant's ACMG classification, automatically calculated by Franklin
The variant's Confidence metric, which takes into account QC, calling, and alignment metrics, as well as allele balance.
Genotype-phenotype correlation, considering the HPO terms introduced by the user in the Case Details section.
The inheritance mode of the diseases associated with the gene.
To learn more about Franklin's prioritization engine, check out Franklin's AI-based variant prioritization engine article.
Variants in the workbench short list are ready for evaluation. Important high-level information regarding the variant appears in the variant tile, for quick and immediate assessment:
The star sign above the variant tile indicates there is relevant information regarding the variant including genotype phenotype correlation or other information which will be highlighted.
Information displayed on SNP variant tile (from left to right):
Franklin's automatic ACMG classification (color-coded circle)
Variant annotation: gene, sample zygosity, c., p.
Aggregated frequency from gnomAD
Internal frequency, from your own repository of cases
Community frequency, by number of cases (heterozygote and homozygote)
Confidence (failed, low, medium, high), and allele balance (%VAF- Variant Allele Frequency)
Aggregated prediction from in silico prediction tools
Gene inheritance
ClinVar classifications
Information displayed on CNV variant tile (from left to right):
Franklin's automatic ACMG classification
Variant annotation: region or genes in region (full list available by hovering the region), CNV type.
Occurrences from DGV and gnomAD
Internal occurrences, from your own repository of cases (50% reciprocal overlap considers a match)
Dosage sensitivity per region
Confidence
Gene inheritance, for all the genes included in the copy number region.
The bottom section of each tile displays the genome coordinate and a link
to the IGV browser (desktop or Franklin's browser).
On the bottom right, you'll find information about the variant, including which filters apply to it and whether it is currently displayed in the workbench.
variant comment will also be displayed here.
Upon clicking on the arrow located on the right-most edge of the tile, Franklin shows an expanded view, with more details regarding the different insights from a wide range of databases.
Clicking the gene name or "Full detail view" button opens the Variant Interpretation hub. This popup centralizes variant, gene, and condition evidence from over 100 databases in Franklin, including exclusive Franklin Community information.
For more information regarding this view, go to Assessment tools overview article.
You can now classify all variants of interest, including those for reporting and those intended for your organization's internal knowledge base.
Classification and interpretation pop-up window will appear after clicking on the "Classify variant" flag 
at the variant tile right end.
You can save the classification as internal, or share it with the rest of the Franklin Community (which is not required but highly encouraged).
After reviewing the workbench shortlist and completing the lab assessment workflow, you can now conclude which variants to report and drag the variants from the workbench to one of the reporting bins.
Reporting bins are configurable and reflect the report categories that your lab defines.
Still have questions? Reach out to our Support Team, they'll be happy to help!