5. Plotting CNV DataΒΆ

Now that we have performed sample-level QC, we can plot our CNV calls, along with the relevant evidence.

To switch from the sample table to the CNV table:

  • Select CNVs from the dropdown above the currently open table.
CNV Table

Figure 5-1. CNVs Table View

While this table provides many useful pieces of information associated with the CNV calls, plotting the CNV data associated can be helpful when performing analysis. Before plotting, though, the CNV State column can be queried to exclude missing values. This is done by right clicking on the CNV State column header and select Query Column Values.

Query CNV State column header

Figure 5-2. Query CNV State Column Values

This opens up a filter tag in the title header. Here, click on the question mark to present options for the query.

Query CNV State column header question mark

Figure 5-3. Query CNV State Column Values Header

Checking all of the options here will keep them in the column, and then remove any missing values. The selection of all options (which are ‘Het Deletion’ and ‘Duplicate’ in this example). The selected options will now appear in the query filter in the header, and clicking anywhere on the screen not on the value query selection window will set the currently selected configuration and close the window.

Query CNV State column header selection

Figure 5-4. Query CNV State Column Values Selection

Once the missing CNV State values are eliminated, the CNV State field can be plotted. To plot the CNV State for the current sample:

  • Right click the CNV State column
  • Select Plot for Current Sample
Plot for Current Sample

Figure 5-5. Right-Click Column Menu

This will open a GenomeBrowse view containing the CNV State of the current sample plotted along side the gene track.

CNV State Plot

Figure 5-6. GenomeBrowse window with CNV State

In addition to the CNV state, it is also useful to plot the evidence used to call the CNVs. To do this:

  • Open the coverage table by selecting Coverage Regions from the table selection menu.

This table contains the CNV data associated with each target region. This includes the regional CNV state, QC flags, Ratio, Z-score, and the number of variants for which VAF was considered.

The two primary pieces of evidence used to call CNVs are the Z-score and Ratio.

To plot these fields:

  • Right click on the Z-score column, then select Plot for Current Sample.
  • Then, right click on the Ratio column, then select Plot for Current Sample.
Z-score and Ratio Plot

Figure 5-7. Z-score and Ratio added to GenomeBrowse

GenomeBrowse provides a number of controls that can be used to customize the appearance of the plots. We will use these controls to add a mid step connector to our Ratio and Z-score plots.

To access the control menu for a plot:

  • Right click the Z-score plot
  • Select Controls... from the pop-up menu
Plot Controls

Figure 5-8. Open Plot Controls

This will display a control panel to the left of the GenomeBrowse view. From this panel:

  • Click the dropdown labeled Connector and select Mid step.
Connector Control

Figure 5-9. Plot Controls

This will add a mid step connector to the currently selected plot. Repeat these steps for the Ratio plot.

Mid Step Connector

Figure 5-10. Mid Step Connector for both plots