Table 3 Description of predicted CNVs.
From: Benchmarking germline CNV calling tools from exome sequencing data
Algorithm | Number of CNVs | Deletion | Duplication | Target* | Mean of targets** | Total length of CNVs, kb | Mean CNV length, kb | CNV size range, kb |
|---|---|---|---|---|---|---|---|---|
CANOES | 16 | 16 | 0 | 306 | 19 | 3583.4 | 51.5 | 0.4–2056.1 |
CLAMMS | 34 | 13 | 21 | 62 | 2 | 122.6 | 3.6 | 0.1–77.7 |
cn.MOPS | 38 | 29 | 9 | 276 | 7 | 2207.9 | 21.5 | 1.8–886.8 |
CNVkit | 16 | 16 | 0 | 309 | 19 | 4194.4 | 262.1 | 0.5–1347.4 |
CODEX | 97 | 56 | 41 | 885 | 9 | 8314.7 | 85.7 | 4.4–117.3 |
CoNIFER | 12 | 12 | 0 | 124 | 10 | 343.5 | 15.2 | 2.5–185.1 |
CONTRA | 329 | 244 | 85 | 329 | 1 | 135.8 | 0.24 | 0.1–16.8 |
DeAnnCNV | 2 | 1 | 1 | 7 | 3 | 121.7 | 60.8 | 4.4–117.3 |
EXCAVATOR2 | 236 | 183 | 53 | 5002 | 21 | 40359.8 | 71.6 | 1.4–2741.6 |
exomeCopy | 845 | 790 | 55 | 91059 | 108 | 1,304,244.3 | 1543.5 | 1.2–40,705.9 |
ExomeDepth | 199 | 151 | 48 | 1057 | 5 | 5018.7 | 4.1 | 0.1–693.0 |
ExonDel | 17 | 17 | 0 | 529 | 31 | 849.5 | 50.0 | 6.0–356.1 |
FishingCNV | 1210 | 815 | 395 | 54434 | 45 | 1,115,772.5 | 922.1 | 0.1–26,762.8 |
HMZDelFinder | 7 | 7 | 0 | 15 | 2 | 99.2 | 14.2 | 0.1–63.5 |
PatternCNV | 243 | 233 | 10 | 254 | 1 | 51.2 | 0.2 | 0.0–1.63 |
XHMM | 11 | 8 | 3 | 211 | 16 | 1069.6 | 40.3 | 5.2–534.4 |
