The new VarSeq CNV Caller Tutorial covers the basics of the VarSeq CNV calling algorithm, with an emphasis on visualization and interpretation of results.
This workflow requires an active VarSeq license with the CNV Caller on Target Regions feature included. You can go to Discover VarSeq or email firstname.lastname@example.org to request an evaluation license with the CNV functionality included.
The VarSeq CNV calling algorithm relies on coverage information computed from BAM files. The algorithm uses changes in coverage relative to a collection of reference samples as evidence of CNV events. Using these reference samples, the algorithm computes two evidence metrics: Z-score and Ratio. The Z-score measures the number of standard deviations from the reference sample mean, while the Ratio is the normalized mean for the sample of interest divided by the average normalized mean for the reference samples.
The tutorial will walk you through the following:
- Running the CNV Caller Algorithm
- Performing Sample Quality Control
- Plotting CNV Results
- Interpretation of some example calls
If you have any comments or questions about this new tutorial please let us know!
Additional VarSeq tutorials and resources can be found here.