Import Panel of Normals for CNV Calling

If enabling CNV calling in the DRAGEN Enrichment pipeline, requires a panel of normals. The CNV caller is a reference-based normalization algorithm that uses additional, externally supplied matched normal samples to determine a baseline level from which to call CNV events. These matched normal samples are derived from the same library prep and sequencing workflow that is used for the case sample. The algorithm subtracts system level biases that are not sample specific.

Either build a panel, or use a panel supplied by Illumina (currently available for TruSight Hereditary Cancer Panel only).

Use the DRAGEN Baseline Builder BaseSpace App, which accepts FASTQ, BAM, or CRAM and generates a CNV Baseline file (*.combined.counts.txt.gz file).

It is recommended to use ~50 samples to build the baseline.

1. Download a provided Panel of Normals from the Illumina Support Site, or download the custom panel of normals from the DRAGEN Baseline Builder App.
2. From the control software menu, select Minimize Application.
3. Log in to ilmnadmin.
4. Select Applications, and then select Favorites.
5. Select +Other Locations, and then select Computer.
6. Double-click usr, and then local.
7. Double-click illumina, and then aux_files.
8. Drag the Panel of Normals file (*.combined.counts.txt.gz file) to aux_files.
1. Download a provided Panel of Normals from the Illumina Support Site, or download the custom panel of normals from the DRAGEN Baseline Builder App.
2. From the control software menu, select Minimize Application.
3. Log in to ilmnadmin.
4. Select Applications.
5. Under Favorites, select Terminal.
6. Enter the following command:

cp [/path/to/baselinefile] /usr/local/illumina/aux_file