Table 2.
pyAmpli true and false positive rates.False and true positive rates in percentages before (−) and after (+) pyAmpli germline, somatic and LOH variant filtering with corresponding total variant number for ratio calculation. Germline variants were called with the GATK Unified Genotyper. Somatic and LOH variants were called with VarScan2
| Variant | Filter | True positive rate (%) | False positive rate (%) | Number of variants |
|---|---|---|---|---|
| Germline | – | 39 | 61 | 15,673 |
| + | 64 | 36 | 11,368 | |
| Somatic | – | 29 | 71 | 4028 |
| + | 37 | 63 | 885 | |
| LOH | – | 45 | 55 | 934 |
| + | 81 | 19 | 208 |