How to set the fold-change cutoff when the sample purity is not 100%
Given a sample purity of ![$ X$](img35.gif)
![$ T$](img36.gif)
cutoff![]() |
(19.6) |
For example, if the sample purity is 40%, and you want to detect 6-fold amplifications or deletions (e.g. 12 copies instead of 2, or 2 copies instead of 12), then the cutoff should be:
cutoff![]() |
(19.7) |
Figures 19.57 shows the required fold-change cutoffs in order to detect a particular degree of amplification/deletion at different sample purities. Figure 19.58 zooms in for low-level amplifications and deletions.
Figure 19.57: The required fold-change cutoff to detect amplifications and deletions of different magnitudes, as a function of sample purity.
Figure 19.58: Low-level amplifications and deletions: The required fold-change cutoff to detect amplifications and deletions of different magnitudes, as a function of sample purity.
The Copy Number Variant Detection tool calls CNVs that are both global outliers on the target-level, and locally consistent on the region-level. The tool produces several outputs, which are described below.