Method | Reference | Features | Seven steps of Fig. 1 |
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| | S | D | N | P | 1 | 2 | 3 | 4 | 5 | 6 | 7 |
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HMMcopy | Shah et al. [16] | S | N | N | Y | Y | Y | Y | Y | N | 3 | Y |
Ginkgo | Garvin et al. [58] | S | N | N | N | Y | Y | N | Y | Y | 1 | Y |
AneuFinder | Bakker et al. [50] | S | N | N | Y | Y | Y | N | Y | Y | 3 | Y |
SCNV | Wang et al. [57] | S | N | Y | Y1 | N | Y | N | N | Y | 1 | Y |
CopyNumber | Nilsen et al. [69] | M | N | N | N | Y | N | N | Y | N | 2 | N |
SCOPE | Wang et al. [62] | M | N | Y | N | Y | Y | Y | Y | Y | 1 | Y |
CHISEL | Zaccaria et al. [56] | M | Y | N | Y | Y | Y | N | Y | N | 2 | Y |
SCICoNE | Kuipers et al. [15] | M | N | N | N | Y | Y | Y | N | N | 2 | Y |
- Four features of the methods are highlighted. S, whether the method applies to a single sample (S) or multiple samples simultaneously (M); D, whether the method assumes diploidy of the sample (Y) or not (N); N, whether the method requires genome of a normal cell (Y) or not (N); P, whether the method is parametric (Y) or not (N). Each method is also classified according to which of the seven steps of Fig. 1 it employs. 1, the method applies binning (Y) or not (N); 2, the method applies GC correction (Y) or not (N); 3, the method applies mappability correction (Y) or not (N); 4, the method removes outlier bins (Y) or not (N); 5, the method removes outlier cells (Y) or not (N); 6, the method applies sliding window (1), objective function fitting (2), or HMM (3) for segmentation; and 7, the method calls the absolute copy number (Y) or not (N). “NA” denotes that the step is not applicable to the method
- 1The model is automatically calibrated given the identified normal cells