Question: What are the Long Ranger quality control (QC) metrics and thresholds?
Answer: We currently do not have any documentation that describes all of the Long Ranger QC metrics. Metrics that exceed error/warning thresholds will show up at the top of the Loupe Genome summary page. The best source of information is in the following files within the Long Ranger download (you may need to adjust the version numbers of the paths to match your specific version):
longranger-cs/2.2.2/tenkit/lib/python/tenkit/alarms/alarms-wgs.jsonlongranger-cs/2.2.2/tenkit/lib/python/tenkit/alarms/alarms-common.json