Table 2.
Parliament HS1011 summary
| Source | Method | Data | Reference | Total calls | Total Loci | Assembled Loci | Multi source Loci | Force Called Loci | Solo assembled | Solo forced |
|---|---|---|---|---|---|---|---|---|---|---|
| BreakDancer | Paired End | Illumina HiSeq | [43] | 6,474 | 5,520 | 1,740 | 335 | 194 | 104 | 82 |
| CNVnator | Read Depth | Illumina HiSeq | [44] | 6,232 | 6,197 | 679 | 402 | 130 | 176 | 109 |
| Crest | Split Read | Illumina HiSeq | [45] | 2,490 | 2,219 | 1,636 | 138 | 115 | 8 | 3 |
| Delly | Paired End & Split Read | Illumina HiSeq | [23] | 4,465 | 3,720 | 1,150 | 323 | 196 | 109 | 97 |
| Pindel | Paired End | Illumina HiSeq | [46] | 5,728 | 4,451 | 2,432 | 244 | 359 | 421 | 206 |
| SV-STAT | Reference-guided Assembly | Illumina HiSeq | Methods | 893 | 892 | 754 | 90 | 32 | 9 | 1 |
| Tiresias | Consensus Sequences | Illumina HiSeq | Methods | 1,354 | 1,347 | 269 | 36 | 112 | 76 | 110 |
| Spiral | Local Assembly | Illumina HiSeq | Methods | 1,886 | 1,881 | 1,626 | 100 | 98 | 76 | 14 |
| Illumina HiSeq Total | 29,522 | 17,765 | 3,751 | 788 | 814 | 979 | 622 | |||
| PBHoney | Local Error and Tail Mapping | PacBio RS | [27] | 10,759 | 10,340 | 5,883 | 483 | 0 | 3,792 | 0 |
| SVachra | Discordant Read Pairs | Illumina Nextera | Methods | 6,208 | 4,785 | 490 | 454 | 211 | 96 | 211 |
| aCGH + SOLiD | Probe Intensity/Read Depth | aCGH | [25,26] | 1,971 | 1,960 | 231 | 452 | 8 | 30 | 8 |
| BioNano Irys | Single-molecule Motif Mapping | Irys | Methods | 0 | 343 | 201 | 142 | 0 | 41 | 0 |
| Total | 48,460 | 31,184 | 7,733 | 1,133 | 1,033 | 4,897 | 841 |
Descriptions and results for each SV-detection method are provided. BioNano Irys data was used only for corroboration, not initial discovery, owing to its large size and propensity to span multiple events.