Filter Decision trees

Franklin is excited to announce the release of a powerful new capability: Filter Decision Trees.

The Filter Tree feature brings a visual and flexible way to build filtration logic. With the new tree builder, you can easily create complex filtering conditions using And/Or logic and merge multiple nodes to form the exact criteria you need. The intuitive canvas empowers you to design any type of logical structure, making the process clearer and more interactive.

Adding labels to the filter trees will create quick filters for seamless use during analysis. Simply connect a filter tree to an assay, and its labels will be available in the corresponding analysis.

Creating new filter trees is done on the assets page, by clicking on "create new".

Currently, Filter Trees are supported for germline cases, specifically for SNVs/indels in single or family cases. Future releases will extend support to CNVs, compound variants, and somatic/tumor analysis. Quick filter labels will be displayed on variants that match the given filter conditions, enhancing visibility and efficiency during variant review.

Migrating from Quick Filters to Filter Trees: All existing quick filters will be automatically converted to Filter Trees and will appear in the tree list. Each quick filter will become its own filter tree, preserving your existing filtration settings. Creating new quick filters directly from the analysis screen is still supported, and a corresponding tree will be generated during the annotation of the next sample for that assay.

This new approach makes filtration logic more flexible and visually intuitive, improving the overall analysis experience.

We hope you find the new Filter Trees valuable in your workflow.To learn more - please visit our help center article.

Feel free to reach out if you have any questions or feedback about this feature!

Enhanced Filtering with ClinVar Evidence

You can now filter on ClinVar evidence across all three record types:

SCV (Single Submission):

Represents a single submission made to ClinVar for the variant. This was the only filter available until now.

RCV (aggregated variant-condition pair):

Represents the classification for the aggregate record for a variant-condition pair. A single variant may have multiple RCVs if it has been submitted for multiple conditions.

VCV (aggregated variant level):

Represents the classification for the aggregate record for a variant. This classification is based on all submissions, and there is only one VCV result per variant. The aggregated result values are determined by ClinVar based on their internal rule set. To learn more, visit: ClinVar Significance Documentation.

How to Use the New Feature- To select which type of record you would like to filter on, simply use the dropdown option. The default value is set to SCV.

Important Notes:

API Enhancements

A new API endpoint has been introduced to allow case creation from an existing sample.

Duo Cases for carrier screening

Improved performance for very large CNVs

In order to improve performance of annotation in very large CNVs (larger than 100Mb or ½ chromosome) - for these variants Franklin will not display the classification rules (in ACMG classification page) or present ClinVar/Decipher submissions.