Method | Window size | Normalization | Segmentation | Contamination | Ploidy |
---|---|---|---|---|---|
BICseq | Manual | Ratio centralization (built-in) | Bayesian information criterion | No | No |
CNVnorm | Manual | GC, smoothing, Ratio centralization (built-in) | Circular binary segmentation | Yes | Yes |
FREEC | CV and Poisson distribution | GC, mappability, Ratio centralization (built-in) | LASSO and dynamic programming | Yes | No |
CNV_seq | Gaussian Ratio and Geary-Hinkley transformation | Ratio centralization (manual) | Consecutive Overlapping windows | No | No |
rSWseq | No need | Ratio centralization (manual) | Smith-Waterman | No | No |
Varscan | Fixed length broke by the gap and significant change | Ratio centralization (manual) | Circular binary segmentation | No | No |
CNVnator | Manual | GC | Mean shift algorithm | No | No |
ReadDepth | Negative binomial | GC, mappability | Circular binary segmentation | No | No |
RDXplorer | Manual | GC | Event wise testing | No | No |
GPHMM | – | – | HMM | Yes | Yesa |
GAP | – | – | Circular binary segmentation | Yes | Yes |
OncoSNP | – | – | HMM | Yes | Yesa |