Feature | BIC-seq2 | Canvas | CNVnator | FREEC | HMMcopy | QDNAseq |
---|---|---|---|---|---|---|
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] |