CNV Informatics Baseline workflow presets

If you use a single sample analysis workflow, you need to use a copy number baseline to detect CNVs. A copy number baseline can be associated with a panel file in the software. If a copy number baseline is not shipped with a panel, you must create a baseline and add it to an analysis workflow.

A CNV Informatics Baseline is used in Ion Reporter™ Software to detect CNVs in samples when using a custom panel. The CNV Informatics Baseline should include at least 20 samples that are not expected to have germline CNVs. Replicate samples can be used but at least 10 unique samples from diverse populations, and preferably more, are recommended if available.

You can either create a baseline and use that baseline as is, or you can augment an existing baseline with more samples then rerun the create baseline step in the Presets screen of the Workflow tab. When a baseline is augmented with samples, new samples are run, the size of each systematic effect that is encoded in the baseline is estimated, and a correction is applied to remove the effect. The added samples must be diverse to capture likely systematic variation.

To use a CNV Informatics Baseline in Ion Reporter™ Software, you can select the baseline preset when you create an analysis workflow. For more information, see Apply a copy number baseline workflow preset to an analysis workflow. You can then use the analysis workflow to call CNVs in the samples.