Table 1. Summary of the main characteristics of 6 copy number analysis tools.
| Software | OS | GUI | Language | External dependencies | Input | Interactive Output | Real-time Filters/Settings | Detects |
| ExomeCopy | L/W/M | NO | R | YES | BAM | NO | NO | CNV |
| ExomeCNV | L/W/M | NO | R | YES | Coverage | NO | NO | CNV/LOH |
| CoNIFER | L | NO | Python | YES | RPKM | NO | NO | CNV |
| ExomeDepth | L/W/M | NO | R | YES | BAM | NO | NO | CNV |
| VarScan2 | L/W/M | NO | JAVA | NO2 | Pileup | NO | NO | CNV/LOH |
| CEQer | L/W/M1 | YES | C# | NO3 | SAM/BAM/ Pileup | YES | YES | CNV/AI/ LOH |
L/W/M: Linux/Windows/MacOS.
1
L/W/M for processing. W is required for visualization and real-time filtering.
2
The Java Runtime is required.
3
The. NET framework Runtime is required. If not present in the system, it is automatically installed during CEQer setup.