# Can I use exome data for CNV detection?

CNV calling from exome FASTQ is done automatically! A prerequisite for this is [defining a Panel of Normals (PON) per each enrichment kit](https://help.emg.illumina.com/emedgene-analyze-manual/settings/organization_settings_-330+/kit-management/panel-of-normals-pon/attaching-a-pon-to-a-coverage-bed-kit) you're using.

A PON aids to set a baseline coverage pattern and account for recurrent technical artifacts that are specific to your workflow. Depth of coverage per each sequenced region is averaged across PON samples; if a significant increase or decrease from this baseline is detected in a test sample, a CNV is called.

### Recommendations for creating a PON to call CNVs from exome data:

1. Samples for a PON should be derived from healthy individuals.
2. In our experience, a PON of at least 40-50 samples yields the best results. A smaller PON is better than nothing, but keep in mind that you may encounter more false positives.
3. You should aim at preparing samples for a PON in a unified manner to avoid the batch effect. Please log differences in library preparation (if any).