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 |