Given a sample purity of %, and a desired detection level (absolute value of fold-change in 100% pure sample) of , the following formula gives the required fold-change cutoff:
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:
Figure 28.25 shows the required fold-change cutoffs in order to detect a particular degree of amplification/deletion at different sample purities. Figure 28.26 zooms in for low-level amplifications and deletions.
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.