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Virtual Panels

Create and manage Gene panels with Franklin, to streamline the case analysis process

Tom Bensimhon avatar
Written by Tom Bensimhon
Updated over a week ago

Introduction

Virtual panels in Franklin are user-defined, version-controlled sets of genes or genomic regions. They provide a structured way to focus an analysis on specific targets of interest. By applying a virtual panel, users can:

  • Filter results: Restrict analysis outputs to variants within the genes included in the panel.

  • Customize Annotation Process: Apply curated information defined at the gene level (for example, selecting which transcript should be used when annotating variants in that gene).

This guide describes how to create a virtual panel, revise an existing one, and apply panels during analysis.

Navigation

To generate a virtual panel, or review the existing panels added to the organization, navigate to the "Knowledge Base" section from the top menu, and then click on the "Panels" tab.

Create a new Panel

  • Choose the "Add" button, and select the "Create Panel" item from the menu

  • Select a meaningful name, and provide additional information on the panel such as the type of samples, clinical domain and phenotypes that are associated with it

Add genes to your panel

  1. Option one: Import Gene List from a TSV file

The recommended way to create a new panel is by importing a list of genes from a TSV file.

For documentation on how to add panels from a file, please follow here

Franklin provides downloadable template files that can be used when creating or updating a panel. These templates include:

  • A simple gene name list – for quickly adding genes without additional curation.

  • A curated gene list structure – an extended format that supports multiple fields for each gene. These fields allow you to define curation details such as the preferred transcript, which enforces transcript selection during the annotation phase when a hard panel is applied.

For detailed instructions on preparing and uploading a gene file to a panel, see the documentation: Uploading a Genes File to a Panel.

2. Option two: Adding a Gene to the panel

Click on the "Add" to choose the "Select genes" option, to add genes from the user interface, tip: you can add multiple genes by comma-separated values (e.g TP53,EGFR)

Your gene panel will be added to the "Organizational Knowledge Base," and you can review it or edit it from there.

Using Panels

Once a virtual panel has been created, it can be leveraged across multiple stages of analysis and reporting. Panels are not only a convenient way to filter case results but also a powerful framework for ensuring analyses are targeted, reproducible, and aligned with organizational curation standards.

Key capabilities include:

Flexible filtering (Soft vs. Hard panels)

Panels can be applied as soft filters, which restrict the visible results to variants within the panel while leaving the underlying analysis unchanged, or as hard panels, which enforce panel definitions during the annotation phase. Hard panels apply curated information such as preferred transcripts, ensuring consistent variant annotation.

Reporting

Panels streamline reporting by automatically scoping the content to the defined set of genes. This allows users to produce focused reports (e.g., a hereditary cancer panel) while maintaining alignment with laboratory or clinical standards.

Quality Control

Panels can be used to track coverage and quality control metrics specific to the defined gene set. This makes it possible to evaluate whether sequencing quality meets the requirements for all relevant genes before finalizing an analysis or report.

Still have questions? Reach out to our Support Team, they'll be happy to help!

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