Quality-based variant detection
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 both SNVs (single-nucleotide variants), MNVs (multi-nucleotide variants) and InDels (insertion and deletions).
Only the variants that are covered by aligned reads will be found, limiting the
size of InDels that can be found by the number of gaps introduced by the mapper.
To run the variant detection:
Toolbox | Resequencing (
) | Quality-based Variant Detection (
)
This opens a dialog where you can select mapping results (
)/ (
)/ (
) or RNA-Seq analysis results (
).
Clicking Next will display the dialog shown in figure 26.4
Figure 26.4: Quality filtering.
Subsections
- Assessing the quality of the neighborhood bases
- Significance of variant
- Ploidy and genetic code
- Merging adjacent variants into one
- Reporting the variants