Main Window – Variant Viewer

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.

Y-axis Select metric to be plotted against the y-axis of the Variant Viewer plot: Allele Frequency, Quality, Read Depth
Color Select metric to be used to color the data: Sample, Subclone
Violin distribution Checkbox to either display or not display violin plots on top of data.

Mean (red)
Checkbox to either display or not display the mean of single-cell VAFs per plot.

Median (green)
Checkbox to either display or not display the median of single-cell VAFs per plot.

Sub-sample cell
Checkbox to either subsample the data (n = 500 for each group) or use all data for visualization purposes.
  • The Variant Viewer plot may be exported by clicking the icon on the top right corner of the window:  . Supported file formats include PNG, SVG, and PDF.