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Table 2 Eight methods for calling CNVs or CNAs

From: Methods for copy number aberration detection from single-cell DNA-sequencing data

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

  1. 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
  2. 1The model is automatically calibrated given the identified normal cells