|
Method
|
Reference
|
Features
|
Seven steps of Fig. 1
|
|---|
| | |
S
|
D
|
N
|
P
|
1
|
2
|
3
|
4
|
5
|
6
|
7
|
|---|
|
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
