Biomedical Genomics Workbench offers three tools for detecting variants.
- Fixed Ploidy Variant Detection () - described in detail in section Fixed Ploidy Variant Detection
- Low Frequency Variant Detection () - described in detail in section Low Frequency Variant Detection
- Basic Variant Detection () - described in detail in section Basic Variant Detection
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.
To run a variant detection tool, go to:
Toolbox | Resequencing Analysis () | 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.
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:
- SNVs - single nucleotide variants
- MNVs - neighbording SNVs, where there is evidence they occur together
- small to medium-sized insertions and deletions - insertions and deletions fully represented within a single read
- replacements - neighboring SNVs and insertions or deletions