DRAGEN Array PGx CNV Calling

Quality Control Recommendations

For PGx CNV calling, it is recommended that 96 or more samples passing LogRDev <= 0.2 are included in the analysis. The metric is provided in the genotyping sample summary file (gt_sample_summary.csv). For more details, see the explanation for the local analysis.

Semi-Custom PGx Products

Running Semi-Custom PGx Analysis on Cloud

Detailed notes on running this analysis for local can be found here. But for cloud, a workaround is necessary because semi-custom product samples are filtered from the BeadChip table in BaseSpace. Follow these steps:

1. Select an existing commercial product configuration (e.g., GDA_PGx-8v1-0_G4 - GRCh38)

2. Kick off an analysis using the Import Sample Sheet option for the semi-custom product samples

Applicable Arrays

For specific product compatibility, see the Product & Analysis Compatibility table.