View Options

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.