Quality-based variant detection
Note: 'Basic Variant Detection' is the new version of the 'Quality-based Variant Detection' where the filtering options have been unified and extended.
The quality-based variant detection in CLC Genomics Workbench is based on the Neighborhood Quality Standard (NQS) algorithm of [Altshuler et al., 2000] (also see [Brockman et al., 2008] for more information). Using a combination of quality filters and user-specified thresholds for coverage and frequency, this tool finds all variants that are covered by aligned reads.
To run the variant detection:
Toolbox | Legacy Tools () | Quality-based Variant Detection (legacy) ()
This opens a dialog where you can select mapping results ()/ ()/ () or RNA-Seq analysis results ().
Clicking Next will display the dialog shown in figure 29.1
Figure 29.1: Quality filtering.
- Assessing the quality of the neighborhood bases
- Significance of variant
- Ploidy and genetic code
- Reporting the variants