We are happy to introduce several enhancements and new features in our latest update:
Tumor Cases: Filter by Lists, ClinVar Aggregation, and Confidence Quality
You can now filter variants in tumor cases using the Variant Lists filter. This allows to exclude or include variants according to their list memberships (using the two modes of the Variant Lists filter - include or exclude). Contact our Support team ([email protected]) to have variant lists set up for your organization.
Additionally, the ClinVar Evidence filter in tumor cases now allows to filter variants by aggregated ClinVar data - reference or variation ClinVar records (RCV or VCV) - in addition to filtering by submission ClinVar records (SCV) and the number of submissions. For more information on ClinVar classifications, please visit: https://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/
Finally, you can now filter variants in tumor cases using the new “Quality” parameter under the Confidence filter. Quality ranges between Failed and High.
Variant Search: Somatic CNV
You can now search for somatic CNV variants in Franklin’s Search tab, using either hg19 and hg38 reference genome versions. This provides a braoder search scope for somatic variants.
New Alt Depth filter & Depth Filter Name Change
This feature is available for 82.1 version and on.
Alternative depth (Alt Depth) refers to the number of sequencing reads that support the presence of the alternative (non-reference) allele at a specific variant position. Filtering by Alt Depth allow to exclude low-confidence variants that have insufficient read support. The Alt Depth filter is now available under the Confidence Section. The Alt Depth filter is now available for SNP variants in single and family-based germline as well as tumor cases.
To enhance clarity, we have renamed the Depth filter to Total Depth within the Confidence filter settings. Below is the updated view of the Confidence filter:
Sample Sheet Upload: Family Case Creation from Existing Samples
You can now create family cases directly from a sample sheet even when one or more family members has an existing analysis. Simply create in the sample sheet a column named "use existing sample", and fill “yes” only for the family member or members (rows) of interest. Following upload, new analyses will be generated seamlessly. For more information, visit germline and somatic sample sheet pages on Franklin’s Help Center.
Quick Filters: Enhanced Management and Operation
You can now control visibility (show/hide), rearrange the order of, or apply quick filters created from filter trees - all from the “Manage Filters" button of the Variants tab. This enhancement allows you to increase your workflow efficiency.
Additionally, you can now edit the name and description of quick filters in the Tree Builder when building a new filter. Click on a quick filter label to open the edit popup, allowing you to rename and modify the name or description of the filter. Additionally, a delete option is available in the edit popup to remove a quick filter if desired.
Finally, Franklin can be configured to automatically add to the workbench structural variants (SV) that passed through specific SV quick filters in the Variants tab. This alleviates your need to manually add such variants to the workbench. Contact our Support team ([email protected]) to apply this configuration.
Coverage Report: Homology Regions Indicator
When viewing a specific gene, exon or kit region in the coverage report, a new column named "Seg dups" is now available, indicating whether regions of inadequate coverage overlap with segmental duplication regions. Regions overlapping with homology regions having a percentage of 0.98 or higher are marked with a "V," while non-overlapping regions are marked with an ”X”.
