The Copy Number Variant Detection tool

To run the Copy Number Variant Detection tool, go to:

        Toolbox | Resequencing Analysis (Image resequencing) | Copy Number Variant Detection (Image cnv_detection5_16_n_p)

Select the case read mapping and click Next.

You are now presented with choices regarding the data to use in the CNV prediction method, as shown in figure 31.22.

Image cnv_detection_step1
Figure 31.22: The first step of the CNV detection tool.

Image cnv_detection_step2
Figure 31.23: The second step of the CNV detection tool

Click Next to set the parameters related to the target-level and region-level CNV detection, as shown in as shown in figure 31.23.

Clicking Next, you are presented with options about the results (see figure 31.24). In this step, you can choose to create an algorithm report by checking the Create algorithm report box. Furthermore, you can choose to output results for every target in your input, by checking the Create target-level CNV track box.

Image cnv_detection_savestep
Figure 31.24: Specifying whether an algorithm report and a target-level CNV track should be created.

When finished with the settings, click Next to start the algorithm.