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 all variants that are covered by aligned reads.

To run the variant detection:

        Toolbox | Resequencing (Image resequencing) | Quality-based Variant Detection (Image snp_detection)

This opens a dialog where you can select mapping results (Image contig)/ (Image multicontig)/ (Image readtrack) or RNA-Seq analysis results (Image rnaseq).

Clicking Next will display the dialog shown in figure 26.5

Image SNP_detection_step2
Figure 26.5: Quality filtering.



Subsections