Table 1.
Comparison of somatic copy number detection tools from whole exome sequencing data
| ADTEX | Control-FREEC | SynthEx | VarScan2 | |
|---|---|---|---|---|
| Programming language | R, Python | C++ | R, Python | Java, Perl, R |
| Sequencing type | WES | WES/WGS | WES/WGS | WES |
| Input files | BAM, coverage | SAM/BAM, pileup | BAM | BAM, pileup |
| Matched normal required | Yes | No | No | Yes |
| Window/binning | Exons | Non-overlapping windows in exons | Non-overlapping windows of genome | Non-overlapping windows in exons |
| Bias correction | No | Optional | NA | No |
| Purity estimate | No | Optional | YES with variant calling | No |
| Segmentation method | CBS | Lasso | CBS | CBS |
| Segmentation annotation | Yes | Yes | Yes | Yes |
| Graphics provided | Yes | Yes | Yes | Yes |
CBS circular binary segmentation