The copy number detection task is used to detect regions of DNA copy number imbalance within the genome for DNA-Seq experiments.   Partek^® Flow^® provides the CNVkit¹ methodology (https://cnvkit.readthedocs.io/en/stable/) to find regions of altered copy number, optimized for targeted resequencing of whole-exome and targeted panels that utilize a hybrid capture approach.  The methodology uses both targeted reads and nonspecific off-target reads divided into bins to determine copy number, subsequently normalizing the data to a pooled reference of control samples and correcting for systematic biases.

CNVkit dialog

The CNVkit task can be found under the Copy number analysis tab in the context sensitive menu when any Aligned reads or Filtered reads data node is selected.  The dialog consists of four sections: Define controls, Select Reference Assembly, Target, and Advanced options (Figure 1).

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Advanced options allows for customization of parameters for CNV detection.  Please refer to the CNVkit documentation (https://cnvkit.readthedocs.io/en/stable/) for details on the available parameters.

CNVkit report

Selecting the Task report for the Copy number data node will provide a table with test samples in the project (non-control) and the number of copy number regions associated with each sample (Figure 2).  Selecting Option columns at the top right of the table will allow for attribute columns to be added to the report. 

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Selecting the chromosome icon  in the view column will link to Chromosome view.  

References

1.  Talevich E, Shain AH, Botton T, Bastian BC. CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing. PLOS Comput Biol. 2016;12(4):e1004873. doi:10.1371/journal.pcbi.1004873

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