Variant Detectors - overview

Biomedical Genomics Workbench offers three tools for detecting variants.

They are designed for the analysis of different types of samples and they differ in their underlying assumptions about the data, and hence in their assessments of when there is enough information in the data for a variant to be called. An overview of these differences is given in figure 19.71.

Image variantcallersoverview
Figure 19.71: An overview of the variant detection tools.

To run a variant detection tool, go to:

        Toolbox | Resequencing Analysis (Image resequencing) | Variant Detectors

If you double-click on one of the tools, a dialog is opened where you can select the reads track or read mapping to analyze.

Image selectreadmapping
Figure 19.72: Select the read mapping that you want to analyze.

Click on the Next button when the reads track or mapping has been added to the right-hand side of the dialog.

The user is next asked to set the parameters that are specific for the variant detection tool. The three tools, their assumptions, and the tool-specific parameters are described later in their respective sections.

All variant detection tools will call: