Franklin offers more than 50 Quality Control (QC) metrics, calculated from various data sources and tailored to optimize different clinical workflows. Some QC metrics are derived from the entire sequenced data, such as whole exome sequencing (WES) or whole genome sequencing (WGS), while others are specific to the selected hard panel.
Metrics that are relevant for virtual hard panels are calculated based on the virtual panel's targeted region list. This list is calculated from the panel's gene list - the regions include all coding exons, plus a 50 bp padding spanning intronic regions for each exon.
Key virtual panel QC metrics:
Example of QC metrics in a virtual panel case
Average Depth: This metric is calculated for both targeted exome and targeted panel regions. For targeted exome, the calculation is based on the configured target bed file. For the targeted panel, it is calculated based on the panel's targeted region list.
Percent of Panel Covered: This metric indicates how much of the virtual hard panel is covered and can be adjusted to show various thresholds.
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.
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