We are happy to introduce several enhancements and new features in our latest update:
View Variants in Alternate Reference
You can now view genetic variants in an alternate reference genome, such as converting between hg19 and hg38 and vice versa. When reviewing a variant, Franklin will display the equivalent nomenclature in the other reference and a link to the variant in the alternate reference in Franklin. The feature is available for both SV and SNV in the Variant Assessment tab of the variant pop up. Example of the alternate reference:
Enhanced Support in Breakend Variants
Following the recent introduction of Manta-detected Breakend variants in Franklin, we have expanded the platform’s capabilities to support more efficient analysis. You can now view the Region Viewer in the Variant Assessment tab of a variant’s popup, add Breakend variants to your Workbench, and filter by position using the Chromosome filter. These enhancements make it easier to explore, manage, and interpret Breakend variants directly within Franklin.
Supporting Short Deletions in Long-Read Sequencing Sniffles2 Output
We have improved the processing of Sniffles2 long-read sequencing caller output, now fully supporting short deletions (<100 bp) as SNP variants.
Aligned Import and Export of Knowledge Base Variant Information
The format of variant export from the Knowledge Base has been updated to align with the import format. Enhancements include standardized column names, inclusion of genome build and classification tags, support for HTML tags in interpretation fields, updated rule formatting, and the addition of custom interpretation fields for both SNP and CNV data.
Orthogonal Confirmation API Includes Reference Genome Version
You can now retrieve the reference genome build data of a case within the JSON response of the Orthogonal Confirmation API call. For more details, please visit Franklin API documentation (https://api-docs.genoox.com/).