How to set the fold-change cutoff when the sample purity is not 100%
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:
cutoff | (26.17) |
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 | (26.18) |
Figure 26.26 shows the required fold-change cutoffs in order to detect a particular degree of amplification/deletion at different sample purities. Figure 26.27 zooms in for low-level amplifications and deletions.
Figure 26.26: The required fold-change cutoff to detect amplifications and deletions of different magnitudes, as a function of sample purity.
Figure 26.27: 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.