We are happy to introduce several enhancements and new features in our latest update:
Display of “Closest Exon” Annotation for Non-Exonic Variants
SNP transcript information in germline and tumor (somatic) cases now indicates the closest exon number for variants in non-exonic regions (splice donor, splice acceptor, splice region, upstream, downstream, intronic; intergenic variants do not have transcript information displayed). This change presently impacts the closed variant tile, as well as the variant row in Table View of the Variants tab. Example view of the closed variant tile:
This change in display will also be applied to the open variant tile and variant popup in an upcoming version. The new display ensures exon, closest exon, or no annotation is shown according to the region of the variant, providing clearer and more accurate transcript information display for SNPs across Franklin.
QC Metric for Large ROH
In germline cases, the Quality Control tab of the Workbench can now include a new metric - ROH Threshold. This metric includes a configuration for ROH size, and the number of ROH of that size. If ROH above this configured threshold are detected in the case, a warning will be displayed. For example, the ROH Threshold QC metric can be configured to display a warning when at least one ROH, of at least 5000 Kb in size, is detected in the case. Contact our support team ([email protected]) to configure this QC metric for an assay.
Tumor Cases: Additional Parameters for TMB Calculation
In tumor (somatic) cases, we have introduced two new parameters for configuring the TMB biomarker calculation, allowing the calculation to include or exclude variants prevalent in COSMIC, as well as to include or exclude splice region variants. To modify your TMB calculation in Franklin using these parameters, please contact our support team ([email protected]).