The Assays page gives provides visibility into their organization's assays, including each assay's bioinformatic pipeline, Workbench configuration, Variants page filters, and report settings. Organization administrators can also edit the Workbench configuration directly from the assay page.
Who Can Access
All Franklin Premium users can view assay details.
Admin users can also edit the Workbench configuration.
The Assays page is a Franklin Premium feature. If your organization does not have access, contact [email protected].
Accessing the Assays Page
Go to Franklin's main menu (upper-right corner of the application).
Select Assets.
Click View All Assays from the Assays tile.
The All Assays Page
The All Assays page displays all of the assays configured for your organization. Use the search bar at the top of the page to find a specific assay by name.
Viewing an Assay
Click any assay tile to open its details page. The page header displays basic assay information:
Assay name - the name of the assay.
Last updated on - the date of the most recent change.
Last updated by - the user name who made the most recent change.
Analysis type - the assay's analysis type, for example Germline analysis.
Credits per sample - number of credits used for analyzing a sample using the assay.
Use the left navigation panel to browse the assay's configuration sections.
Bio-informatic Pipeline
The Bio-informatic Pipeline section lists the variant files associated with the assay. The list is automatically filtered by the assay's reference genome version (e.g., hg19 or hg38) and analysis type.
The Bio-informatic Pipeline section displays the assay resources and configuration fields associated with the assay's upstream analysis setup. The values available in this section are filtered by the assay's analysis type and selected reference genome. This section includes the following fields:
Expected file format: The expected input file type for the assay, for example FASTQ.
Target BED file: The name of the BED file that defines the assay’s targeted regions.
Reference: The assay reference genome version, HG19 or HG38.
Hard panels: Hard panels applied by the assay.
Default virtual panels: Virtual (soft) panels applied by the assay by default.
Custom annotations: Names of Custom Annotations configured for the assay.
Inclusion/Exclusion variant list: The variant list or lists associated with the assay.
Workbench
The Workbench section displays the Workbench configuration applied to cases that use this assay.
It includes four configuration toggles:
Filter Workbench by virtual panels: When set to Yes, only variants associated with the case's active virtual (soft) panels appear in the Workbench.
Secondary findings default: Determines whether variants related to secondary findings are included (Opt-in) or excluded (Opt-out) in the Workbench by default.
Default Workbench variants: Determines whether Franklin's default Workbench variants are included (Opt-in) or excluded (Opt-out) in the Workbench. If Opt-in is selected together with an active inclusion quick filter, the Workbench will include both the filter's variants and Franklin's default Workbench variants. This configuration can also be overridden per case type or variant type if your organization uses a custom configuration provided by the Franklin team.
Filter Workbench by priority: When set to Yes, only variants above Franklin's priory threshold will be included in the Workbench.
The Active quick filters sub-section shows the Workbench inclusion and exclusion filters configured for the assay, organized into eight fields across two columns:
Inclusion: Single SNP, Family SNP, Single SV, Family SV
Exclusion: Single SNP, Family SNP, Single SV, Family SV
Variants Page
The Variants Page section lists the quick filters applied to the Variants page for cases that use this assay. Filters are grouped by category: Single SNP, Family SNP, Single SV, and Family SV.
Report
The Report section displays the report export format configured for this assay.
Editing the Workbench Configuration
Admin users can edit the Workbench configuration directly from the assay page. Edit Assay is visible in the upper-right corner of the page. To edit the Workbench configuration:
Click Edit Assay in the upper-right corner of the assay page. The page enters Edit Mode.
Make your changes:
To add a quick filter: Click + Add filters in any of the eight filter fields. In the popup, select one or more filters from the list and click Add. An added filter appears as a chip in the field.
To remove a quick filter: Click the × button on a filter chip in any field.
To change the Default Workbench variants or Filter Workbench by priority setting: Click the desired option (Opt-in / Opt-out, or Yes / No).
When you are done, click Save Assay to apply your changes. Saving redirects you to the All Assays page. To discard your changes, click Cancel.
Effect of Changes on Cases
Changes saved to the Workbench configuration take effect as follows:
New cases: Changes apply to any new case created after the assay is saved.
Existing cases: Changes apply to an existing case the next time its Workbench is recalculated. Workbench recalculation occurs when phenotypes or soft panels are added or removed, or when the case is reanalyzed.
Still have questions? Reach out to our Support Team, they'll be happy to help!