We are happy to introduce several enhancements and new features in our latest update:
Filter and Export of CNV Variants by gnomAD Occurrences
In germline cases, a new filter has been added to allow filtration of CNVs by the number of occurrences in gnomAD. The filter is available in the Occurrence filter section of the Variants tab (specifically, the SV tab):
Additionally, export from the SV tab now includes the “gnomAD Occurrences” column, containing the number of occurrences per variant.
Tumor Cases: Filter for Same Amino Acid Change
In tumor (somatic) cases, a new filter has been added to identify missesne variants with the same amino acid change as a known pathogenic or likely pathogenic variant in ClinVar. You can now filter for variants based on this criterion, enhancing the process of variant triaging. The filter is available in the ClinVar Evidence filter section of the Variants tab:
Support for Manta Caller Breakend Detection
As part of our ongoing Franklin/Manta compatibility improvements, breakend variants detected by the Manta SV caller are now supported. A breakend variant represents one side of an SV breakpoint, where the precise location or pairing may be complex or ambiguous and hence calling as a deletion or duplication is not possible. The breakend variant tile shows information on mate position and mate depth available. Breakend variants are filterable using the existing Variant Type filter.
Enhanced Support for RNA and CMA Workflows
Franklin now supports the the import of fusion variants as a part of the TruSight RNA workflow. This includes mapping of confidence information to the variant’s expanded tile and pop-up.
Additionally, the CytoSNP 850K CMA workflow now supports showing the Mosaic indication on the CNV variant tile. Mosaic variants are filterable using the existing Mosaic option in the Variant Type filter.
API for Creating and Updating Panels
You can now create and update Knowledge Base gene panels using Franklin API . The API supports creation of new panels, as well as updating existing panels - appending genes, or replacing (overwriting) the panel’s entire gene list. The API response includes panel details as well as a download link and a optional list of all panels. For more details, please visit Franklin API documentation (https://api-docs.genoox.com/).
Automatic Failure Marking for Analyses
Analyses now automatically show an Error indication if their pipeline processing or annotation fails. This indication on the case tile replaces the previously presented static progress bar.
Display Last Case Details Update Information
You can now view the date, time, and username of the last update for case details. This information is located at the bottom-right corner of the case details, below the “Creator” section. If no updates have been made, these fields will not be displayed.
