|Show samples||Lists all samples that are loaded. Samples may be selected or deselected by highlighting them with the mouse cursor.|
|Show subclones||Lists all subclones that are identified with all selected variants. Subclones may be selected or deselected by highlighting them with the mouse cursor.|
|Show||(De)-select violin distribution plots, mean (red), median (green), or sub-sampled cells (10% of data displayed).|
|Plot grouping||Visualizes subclones on a per-sample basis and/or per-subclone basis. Individual samples or subclones are color-coded differently, respectively.|
|First group by||Only available if samples and subclones are selected in Plot grouping option.|
|Y-axis||Displays one of the three data: Allele Frequency (default), Genotype Quality, Read Depth.|
|Color the||Colors either sample or subclone specific.|
The Variant Viewer provides additional quantitative metrics for each variant to help assess its quality and validity. Information of a variant that is highlighted in the Variants table will be shown in this section.
In particular variant-specific allele frequency distributions may be reviewed either across a set of samples, subclones, or both. Each dot represent a cell. Data may be color-coded by sample or subclone. (1) Allele Frequency (VAF), (2) Genotype Quality or (3) Read Depth may be plotted as a function of either subclone or sample.