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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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Define controls allows for the specification of control samples in the project that will be pooled to create a reference copy number for both on- and off-target genomic bins using  bias-corrected read depth from each control sample.  In projects that contain matched tumor/normal samples, all normal samples should be included in the control sample pool.  Control samples can be group based on a categorical attribute in the data tab or manually selected. If no control samples are available, it is possible to run CNVKit with no controls by leaving the sample pool empty. 

Select reference sequence will utilize the species genome build utilized for alignment.  If the selected aligned data node was imported, the reference assembly used during data alignment needs to be specified from the drop-down list.  The Assembly can be previously associated with Partek^® Flow^® via Library File Management or added on the fly.

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