How to run the InDels and Structural Variants tool

To start the structural variant detection:

        Toolbox | Resequencing (Image resequencing) | InDels and Structural Variants tool (Image structuralVariationDetection_16_n_p)

This will open up a dialog. Select the read mapping of interest as shown in figure 26.18 and click on the button labeled Next.

Image indels_and_structuralvariation_step2
Figure 26.18: Select the read mapping of interest.

Specify the settings shown below and in figure 26.19. For further details about these settings, please see Creating Left- and Right breakpoint signatures.

Image indels_and_structuralvariation_step3
Figure 26.19: Select the relevant settings.

Clicking on the button labeled Next opens up the "Results handling" dialog (figure 26.20) with the following output options:

Image indels_and_structuralvariation_step4
Figure 26.20: Select output formats.