Table 1 Summary of features for the algorithms

Language

C++, Perl, R

C#

C++

C++, R

C++, R

R

Input format

BAM

BAM

BAM

BAM, many other

BAM

BAM

Control sample

optional

optional

no

optional

optional

yes

User-defined/built-in window size

built-in

built-in

user

both

user

user

Fixed window size

yes

no

yes

yes

yes

yes

GC-correction

yes

yes

yes

yes

yes

yes

Mappability correction

yes

no

no

yes

yes

yes

Sex-determination

From XY CNVs

From XY CNVs

From XY CNVs

User-specified

From XY CNVs

From XY CNVs. By default, XY excluded.

Segmentation

BIC¹

Haar wavelet (default), CBS²

Mean shift

LASSO³

HMM⁴

CBS²

Version

0.2.4, 0.7.2

1.11.0

0.3.3

11.0

1.20.0

1.14.0

Reference

[20]

[21]

[22]

[23]

[24]

[25]