How can I visualize variant calls?
The Singular Analysis Toolset provides several methods to help users visualize variant calls. For example:
- QC Visualization in vcAutoAnalysis allows users to display histograms of distributions of DP, GQ, AF, and VSN (the minimum sample number per variant) in variant calls and helps users to determine reasonable thresholds to remove low-quality variants.
- Unsupervised hierarchical clustering analysis by the vcHC function allows users to display clustering relationships in samples and variants and to select sample groups and variant groups of interest for subclonal analysis.
- Manhattan plots allow users to display and select variants with statistical significance between defined case and control groups by Fisher’s exact test.