Panel of normals (PON)

For detecting copy number variation (CNV) in targeted panel and exome cases, DRAGEN utilizes a Panel of Normals (PON) approach. This method leverages a set of matched normal samples to establish a reference baseline for CNV event detection.

A PON file is typically a text file listing absolute paths to 'target counts' files of individual matched normal samples. However, a PON can also be in the form of a combined counts file, which is a column-wise concatenation of individual target counts files (either GC-corrected or not).

The Illumina BaseSpace Baseline Builder App can generate this combined counts file (see the section "Creating a PON for Emedgene Using BaseSpace Baseline Builder").