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Capabilities of RNAseq-based DNA copy number calling algorithms
| Per-sample runtime | Arm/Chromosomal CNV | High aneuploid adjustment | Gene-level CNV | |
|---|---|---|---|---|
| RNAseqCNV | 10 minutes | Yes | Yes | No |
| CNVkit | 74 minutes | No | No | Yes |
| CaSpER | 14 minutes | Yes | No | Yes |
| SuperFreq | 2 hours | No | Yes | Yes |
Table notes: Per sample run time refers to average per-sample runtime on a standard PC, except SuperFreq on an high performance computing server
