Table 2.
Comparison of CNVs detected from simulated sequence reads with known 885 CNVs of NA12878 by five different methods with different methods of alignments.
| Alignment | MATCHCLIP | CREST | PRISM | PINDEL | DELLY |
|---|---|---|---|---|---|
| ERR_RATE = 0.0 | |||||
| bwa PE | 758:17 | 632:2 | 594:80 | 696:158 | 798:291 |
| bwasw | 705:26 | 652:9 | |||
| bowtie2 PE | 781:18 | 642:6 | 580:76 | 719:165 | 496:146 |
| bowtie2 SE | 728:2 | 635:1 | |||
| novo PE | 758:8 | 414:2 | 577:26 | 681:123 | 769:223 |
| novo SE | 691:3 | 124:2 | |||
| ERR_RATE = 0.02 | |||||
| bwa PE | 738:12 | 631:32 | 586:42 | 644:71 | 781:301 |
| bwasw | 653:55 | 643:12 | |||
| bowtie2 PE | 770:26 | 645:21 | 559:59 | 666:85 | 509:154 |
| bowtie2 SE | 723:1 | 633:3 | |||
| novo PE | 708:4 | 312:2 | 576:21 | 657:60 | 762:226 |
| novo SE | 669:3 | 118:0 | |||
The numbers in each cell are given in the format “concordant CNVs:false positives”.