The Variant Viewer provides additional quantitative metrics for each selected variant to help assess its quality and validity. Click in the horizontal box with the words Variant Viewer to display the viewer.
Each dot represents a cell, and the data display is customizable by altering the option settings. For example, variant-specific allele frequency distributions may be reviewed either across a set of samples, subclones, or both. The allele frequency, quality, or read depth can be plotted as a function of either the sample or subclone.
The Export button in the top-right corner allows you to export the filtered data, selected data, and violin plot.
Refer to this section for more information about the .zip file created when exporting filtered data or selected data.
Exporting a violin plot generates a single .png, .pdf, or .svg file.
Settings: Click the icon to customize the information displayed for the selected variant.
Show samples: Lists all loaded samples. Check to select which samples to display.
Show subclones: Lists all subclones identified with the selected variant. Check to select which subclones to display.
- Violin distribution: Check to display the violin plots on top of the data.
- Mean (red): Check to display the mean of single-cell VAFs per plot as a horizontal line.
- Median (green): Check to display the median of single-cell VAFs per plot as a horizontal line.
- Sub-sampled cells: Check to subsample the data (500 for each group) or use all the data for visualization purposes.
Plot grouping: Plot by sample, subclone, or both.
First group by: Choose which to group by first – Sample or Subclone.
Y-axis: Select which metric to plot against the y-axis – Allele Frequency, Quality, or Read Depth.
Color the: Select which data to color – Sample or Subclone.