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Version 88 Updates

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Written by Support
Updated today

We are happy to introduce several enhancements and new features in our latest update:

Mapping Quality Threshold for SNP Calling

In single or family germline analysis, assays that include SNP calling via FreeBayes can now be configured with a custom mapping quality (MQ) threshold. This feature is particularly relevant for calling variants located in genomic regions of high sequence homology, where reads may map ambiguously to multiple loci. Such variants are often called with a mapping quality of zero (MQ0) because their true genomic location cannot be confidently determined. When an assay is configured with an MQ threshold of 0, the MQ0 variants will be called and displayed with a highlight that indicates their nature, including that they may be false or have a false location:

To configure this in your assay, please contact our support team ([email protected]).

AI-Based Evidence Type Annotations in Publications

AI-based evidence type annotations are now displayed for publications in the Publications tab. The annotations are shown as highlighted labels alongside other publication highlights, making it easier to quickly identify and distinguish publications based on evidence type - including Allelic Data, Case Control Data, De Novo Data, Other Observational Data, and Functional Data.

We would be glad to receive your feedback about these annotations. Please use the “Raise an issue” button at the top of the Publications tab.

SNP Export via Email

In germline cases, when exporting any number of SNPs from the Variants tab, the variants will now always be exported via email instead of browser download. The email contains a download link for a CSV file, which includes all of the columns as previously available in the CSV files of the two export methods. The combined file therefore provides more complete information in SNP export from the Variants tab.

Dynamic Snippets

You can now embed dynamic parameters into your snippets. This enhancement allows Franklin to automatically insert variant- and case-specific details, such as HGVS notation, zygosity, gene name, and more - directly into your text. Dynamic snippets are supported across the variant interpretation snippet types. This feature helps reduce manual entry, ensures consistency, and speeds up interpretation workflows. For more information on dynamic snippets, please visit the relevant article on Franklin Help Center.

Variant Links Widget

We have added a new Links widget to the Variant Assessment tab in all case types and search views for SNP variants. The widget provides default external resources like ClinVar, gnomAD, and UCSC:

The widget additionally provides custom linkouts that can be configured based on your organization’s needs, and the custom linkouts can be set to appear only in the widget, helping to clear space from the variant header and streamline the interface. Custom linkouts can be configured for your organization by contacting our support team ([email protected]).

New Report Export API

A new API for exporting the Report is now available. Similar to the existing API, the new API provides the ability to retrieve reports in JSON format. Unlike the existing API, the new API outputs reported variants in a binned structure that reflects variant bin assignments in the Workbench. It also includes considerably richer information, not available previously. The existing report export API remains available and unchanged but will no longer be updated. For additional information, refer to the Franklin API documentation (https://api-docs.genoox.com/).

Tumor Cases: Arriba Caller for Fusion Variants

Tumor (somatic) cases can now include fusion variant calling using the Arriba calling pipeline, now integrated in Franklin. Arriba supports fusion calling from RNA-only or RNA+DNA sequencing data, and can perform UMI trimming. This enhancement therefore allows to perform both secondary and tertiary analyses of Fusion variants from different kits directly in Franklin, increasing workflow efficiency. To include Arriba calling in your assay, please contact our support team ([email protected]).

Tumor Cases: Fusion Transcript Annotation Update

In tumor (somatic) cases, to increase the consistency and accuracy of fusion variant annotation, the annotated transcript for fusion variants is now the canonical transcript as included in the MANE Select dataset. This update may change the annotation of exons for a fusion variant’s breakpoints; most fusion variants are not expect to be impacted by this update.

Coverage of Single-Gene Hard Panels Calculated by Preferred Transcripts

For organizations that have preferred transcripts configured, in cases created from sample sheet or API, the coverage calculations for single-gene hard panels now use the preferred transcripts (similar to the existing calculations for hard panels originating from the Knowledge Base). This enhancement ensures that QC metrics and the Coverage Report fully reflect your organization’s transcript preferences. Reminder: organization-preferred transcripts can be configured by contacting our support team ([email protected]).

Enhancement of Manually Adding Variants to Case

In germline and somatic cases, we have added support for manually adding CNVs to SNP-only cases, or SNPs to CNV-only cases. This previously restricted ability is now fully supported, enabling variants from different testing modalities to be reviewed, interpreted, and reported in a single case in Franklin.

Bug Fixes:

Visual Feedback on Sample Drag-and-Drop in Family Analysis

Fixed an issue in family analysis case creation from the UI, where canceled, out-of-bounds, replacement, or fast drags of an unassigned sample from Sample Repository rendered the sample greyed-out in Sample Repository.

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