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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