How to set the fold-change cutoff when the sample purity is not 100%

Given a sample purity of $ X$%, and a desired detection level (absolute value of fold-change in 100% pure sample) of $ T$, the following formula gives the required fold-change cutoff:

cutoff$\displaystyle = \frac{X\text{\%}}{100\text{\%}} \times T + (1-\frac{X\text{\%}}{100\text{\%}})$ (21.6)

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$\displaystyle = \frac{40\text{\%}}{100\text{\%}} \times 6 + (1-\frac{40\text{\%}}{100\text{\%}}) = 3.0.$ (21.7)

Figures 21.35 shows the required fold-change cutoffs in order to detect a particular degree of amplification/deletion at different sample purities. Figure 21.36 zooms in for low-level amplifications and deletions.

Image sample_purity_graph_1
Figure 21.35: The required fold-change cutoff to detect amplifications and deletions of different magnitudes, as a function of sample purity.

Image sample_purity_graph_2
Figure 21.36: 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.