Franklin offers a comprehensive set of more than 50 specialized Quality Control (QC) metrics, tailored to optimize various clinical workflows. This article aims to highlight the key metrics that are relevant to the virtual panels workflow.
The metrics in Franklin are calculated based on different data sources. Some metrics are derived from the entire sequenced data, such as whole exome sequencing (WES) or whole genome sequencing (WGS). Other metrics are specific to the selected hard panel.
Here are the important metrics to emphasize:
Example of QC metrics in a virtual panel case
Average Depth: This metric is calculated for both targeted exome and targeted panel. For targeted exome, the calculation is based on the configured target bed file. For targeted panel, it is calculated using the gene list from the hard panel, which includes an exon padding configuration. Alternatively, it can be calculated based on the pre-configured bed file for the hard panel.
Percent of Panel Covered: This metric measures the coverage of the hard panel and can be adjusted to display different thresholds. It is calculated using the hard panel data.
Other metrics in Franklin can be configured to utilize either the WES/WGS data or the hard panel data, depending on the specific requirements of the analysis.
It's important to note that QC does not consider soft panels that can be changed during the case analysis. These panels are not used for quality control purposes.
By leveraging Franklin's extensive QC metrics, researchers and clinicians can ensure the accuracy and reliability of their virtual panel workflows.
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