Table 1.
Comparison between Alleloscope and CHISEL using two benchmark strategies.
| Dataset | Method | Sensitivity | Specificity |
|---|---|---|---|
|
| |||
| Benchmark with matched linked-read sequencing data | |||
|
| |||
| P5915 | Alleloscope | 0.9373 | 0.9915 |
| CHISEL (before correction) | 0.7284 | 0.9757 | |
| CHISEL (after correction) | 0.7786 | 0.9722 | |
| P5931 | Alleloscope | 0.9402 | 0.9986 |
| CHISEL (before correction) | 0.7520 | 0.9434 | |
| CHISEL (after correction) | 0.0112 | 0.9508 | |
| P6198 | Alleloscope | 0.9433 | 0.9666 |
| CHISEL (before correction) | 0.9397 | 0.9311 | |
| CHISEL (after correction) | 0.9700 | 0.9359 | |
| P6335 | Alleloscope | 0.9671 | 0.9906 |
| CHISEL (before correction) | 0.7858 | 0.9873 | |
| CHISEL (after correction) | 0.8404 | 0.9943 | |
| P6461 | Alleloscope | 0.8638 | 0.9904 |
| CHISEL (before correction) | 0.7932 | 0.9624 | |
| CHISEL (after correction) | 0.8143 | 0.9411 | |
|
| |||
| Benchmark with subsampling | |||
|
| |||
| 50% subsample | Alleloscope | 0.9261 | 0.9905 |
| CHISEL (before correction) | 0.9267 | 0.9383 | |
| CHISEL (after correction) | 0.9496 | 0.9446 | |
| 25% subsample | Alleloscope | 0.8249 | 0.9525 |
| CHISEL (before correction) | 0.6515 | 0.6412 | |
| CHISEL (after correction) | 0.6533 | 0.6475 | |