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 Biomedical 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 (Image legacy_tools) | Quality-based Variant Detection (legacy) (Image snp_detection_legacy_overlay_16_n_p)

This opens a dialog where you can select mapping results (Image contig)/ (Image multicontig)/ (Image read_track_16_n_p) or RNA-Seq analysis results (Image rnaseq).

Clicking Next will display the dialog shown in figure 33.1

Image SNP_detection_step2
Figure 33.1: Quality filtering.