Version 87 Updates

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

We enhanced our support of Agilent CGH workflows under Franklin’s CMA solution category. We have added support for creating CMA cases using a CGH assay that does not include SNP probe information. This addition joins Franklin’s existing support of Agilent CGH array that utilizes SNP probes. To configure a CGH assay for your organization, please contact our support team ([email protected]).

To improve clarity, the “Save” button in the Variant Classification wizard is now labeled “Submit”. The functionality remains the same - you can still submit classifications as either draft or final. This is a small wording change to better match how the action is used.

When variant quality in a VCF is denoted as ".", the variant will now be displayed and filtered as "N/A" instead of "0" quality. This change is effective for new cases, as well as for existing cases following re-annotation, across Franklin. The change will be reflected in the variant display, and is expected to change results of the Quality and Quality by Depth filters. Specifically, SNP that previously passed these filters when filtering for Low quality, will now pass when filtering for Failed quality (or pass when the “Include N/A” filter option is used). Similarly, SV that previously passed the Quality filter when filtering for 0 quality, will now pass when the “Include N/A” option is used.

In duo carrier screening cases (where a “virtual proband” is created from the parents’ variants) if one or both parents have BAM files included in the case, the variants of the “virtual proband” can now be opened in desktop IGV for display with the parental BAM files. Use “Open in desktop IGV” from the tile’s location icon to open a variant in desktop IGV. For more information on Duo cases, please visit the following Franklin Help Center article. Contact our support team ([email protected]) to enable Duo cases for your organization.

In tumor (somatic) cases, new QC metrics can now be configured in cases created using the STAR-Fusion calling pipeline. The new metrics are the total number of reads, and the number of reads mapped to reference. Contact our support team ([email protected]) to configure this QC metric for an assay based on STAR-Fusion.

In tumor (somatic) cases, the “Download BAM” case-level option now enable the download of RNA BAM, in both RNA-only cases and DNA+RNA cases.

Resolved a rare issue in Variants tab, where on some occasions, a lower number of variants was displayed after performing a browser page refresh, if the applied quick filter included the Panel filter.