Table 1 Program SNV Detection Results for (a) ClinSeq samples and (b) 1000 Genomes samples
From: Evaluation of variant detection software for pooled next-generation sequence data
a | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
4 PooledSamples | %Sen | %FP | %BA | %SD | %Sen | %FP | %BA | %SD | %Sen | %FP | %BA | %SD | %Sen | %FP | %BA | %SD |
100 % Sample Covg | 50 % Sample Covg | 25 % Sample Covg | 12.5 % Sample Covg | |||||||||||||
CRISP | 99.2 | 7.8 | 95.7 | 98.9 | 97.3 | 7.3 | 95 | 94.2 | 88.9 | 6.5 | 91.2 | 76.5 | 71.3 | 6.2 | 82.5 | 44.9 |
SNVer | 81.9 | 3.8 | 89 | 72.4 | 74.9 | 3 | 85.9 | 59.1 | 62.7 | 2.4 | 80.1 | 37.3 | 48 | 1.7 | 73.2 | 16.6 |
LoFreq | 97.3 | 8.3 | 94.5 | 95.5 | 93 | 6.7 | 93.1 | 84.1 | 84 | 5.2 | 89.4 | 63.4 | 69 | 4.1 | 82.5 | 39.1 |
VarScan | 46.7 | 0.1 | 73.3 | 4.7 | 47.7 | 0.1 | 73.8 | 6.2 | 48.9 | 0.1 | 74.4 | 8.1 | 45 | 0.3 | 72.3 | 6.6 |
GATK | 99.7 | 6.9 | 96.4 | 99.4 | 98.7 | 7.4 | 95.7 | 96.7 | 94.7 | 8 | 93.3 | 86.3 | 85.7 | 8.7 | 88.5 | 65.1 |
8 Pooled Samples | %Sen | %FP | %BA | %SD | %Sen | %FP | %BA | %SD | %Sen | %FP | %BA | %SD | %Sen | %FP | %BA | %SD |
100 % Sample Covg | 50 % Sample Covg | 25 % Sample Covg | 12.5 % Sample Covg | |||||||||||||
CRISP | 99.3 | 7.8 | 95.8 | 98.9 | 97.2 | 7.4 | 94.9 | 94.1 | 88.9 | 6.8 | 91.1 | 77.5 | 71.2 | 6.7 | 82.2 | 46.1 |
SNVer | 79.9 | 3.6 | 88.1 | 65.7 | 69.4 | 3.2 | 83.1 | 47.1 | 55.5 | 2.8 | 76.3 | 25.3 | 42.5 | 2.4 | 70 | 9.9 |
LoFreq | 96.7 | 7.3 | 94.7 | 93.1 | 91.8 | 6.5 | 92.7 | 79 | 82.8 | 5.4 | 88.7 | 56 | 70.7 | 4.3 | 83.2 | 31.8 |
VarScan | 28.8 | 0.1 | 64.4 | 0 | 29.2 | 0.1 | 64.5 | 0.1 | 29.8 | 0.1 | 64.8 | 0.1 | 30.4 | 0.2 | 65.1 | 0.3 |
GATK | 98.5 | 8.6 | 94.9 | 96.4 | 98 | 8.5 | 94.7 | 95.1 | 94 | 10.1 | 91.9 | 86 | 83.9 | 11.4 | 86.3 | 64 |
16 Pooled Samples | %Sen | %FP | %BA | %SD | %Sen | %FP | %BA | %SD | %Sen | %FP | %BA | %SD | %Sen | %FP | %BA | %SD |
100 % Sample Covg | 50 % Sample Covg | 25 % Sample Covg | 12.5 % Sample Covg | |||||||||||||
CRISP | 99.1 | 7.7 | 95.7 | 98.5 | 96.7 | 7.6 | 94.6 | 93.3 | 87.7 | 7 | 90.4 | 76.6 | 69.3 | 7 | 81.2 | 46.3 |
SNVer | 66.9 | 3.5 | 81.7 | 42.9 | 53.7 | 3.4 | 75.1 | 23.8 | 42.4 | 3.2 | 69.6 | 10.8 | 33.2 | 3 | 65.1 | 3.6 |
LoFreq | 94.9 | 6.4 | 94.2 | 87.6 | 88.5 | 6 | 91.3 | 69.8 | 78.5 | 5.5 | 86.5 | 44.7 | 67 | 4.8 | 81.1 | 22.5 |
VarScan | 18.1 | 0.1 | 59 | 0 | 18.2 | 0.1 | 59 | 0 | 18.4 | 0.1 | 59.1 | 0 | 18.7 | 0.1 | 59.3 | 0 |
GATK | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
32 Pooled Samples | %Sen | %FP | %BA | %SD | %Sen | %FP | %BA | %SD | %Sen | %FP | %BA | %SD | %Sen | %FP | %BA | %SD |
100 % Sample Covg | 50 % Sample Covg | 25 % Sample Covg | 12.5 % Sample Covg | |||||||||||||
CRISP | 98.7 | 7.9 | 95.4 | 97.5 | 95.8 | 7.6 | 94.1 | 91.8 | 86 | 7.1 | 89.5 | 74.4 | 67.5 | 7.3 | 80.1 | 46.2 |
SNVer | 41.8 | 4.2 | 68.8 | 11 | 34.6 | 4.2 | 65.2 | 5 | 29.3 | 3.8 | 62.7 | 2.3 | 24.5 | 3.8 | 60.4 | 0.6 |
LoFreq | 90.7 | 5.4 | 92.7 | 77.5 | 82.2 | 5.4 | 88.4 | 55.7 | 71.1 | 5.3 | 82.9 | 31.2 | 60.5 | 5.2 | 77.6 | 13.8 |
VarScan | 11.4 | 0 | 55.7 | 0 | 11.5 | 0.2 | 55.7 | 0 | 11.5 | 0.2 | 55.7 | 0 | 11.6 | 0.2 | 55.7 | 0 |
GATK | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
b | ||||||||||||||||
4 Pooled Samples | %Sen | %FP | %BA | %SD | %Sen | %FP | %BA | %SD | %Sen | %FP | %BA | %SD | %Sen | %FP | %BA | %SD |
100 % Sample Covg | 50 % Sample Covg | 25 % Sample Covg | 12.5 % Sample Covg | |||||||||||||
CRISP | 99.2 | 4.4 | 97.4 | 98.5 | 90.9 | 4 | 93.5 | 80.3 | 74.2 | 3.7 | 85.3 | 48.7 | 55.5 | 3.3 | 76.1 | 22.4 |
SNVer | 86.5 | 1.3 | 92.6 | 74.8 | 70.9 | 0.9 | 85 | 47.3 | 50.3 | 0.4 | 74.9 | 18.5 | 33.2 | 0.6 | 66.3 | 4.4 |
LoFreq | 96.8 | 0.4 | 98.2 | 94.1 | 87.3 | 0.2 | 93.5 | 73.9 | 71 | 0.1 | 85.5 | 44.3 | 48.9 | 0 | 74.4 | 19.7 |
VarScan | 44.6 | 0 | 72.3 | 0.9 | 45.1 | 0 | 72.5 | 3.2 | 42.3 | 0 | 71.2 | 3.8 | 33.4 | 0 | 66.7 | 1.4 |
GATK | 99.9 | 0.3 | 99.8 | 99.8 | 97.5 | 0.2 | 98.6 | 93.8 | 89.3 | 0.2 | 94.6 | 74.9 | 73.9 | 0.3 | 86.8 | 44.7 |
8 Pooled Samples | %Sen | %FP | %BA | %SD | %Sen | %FP | %BA | %SD | %Sen | %FP | %BA | %SD | %Sen | %FP | %BA | %SD |
100 % Sample Covg | 50 % Sample Covg | 25 % Sample Covg | 12.5 % Sample Covg | |||||||||||||
CRISP | 99.2 | 4.3 | 97.5 | 98.4 | 91.3 | 4.1 | 93.6 | 81.4 | 75.5 | 3.7 | 85.9 | 50.4 | 57.7 | 3.2 | 77.2 | 23.8 |
SNVer | 80.5 | 2.1 | 89.2 | 62 | 61.8 | 1.8 | 80 | 30.1 | 44.5 | 0.8 | 71.8 | 9.3 | 30.6 | 0.8 | 64.9 | 1.6 |
LoFreq | 95.4 | 0.4 | 97.5 | 89.7 | 84.4 | 0.2 | 92.1 | 64 | 68.5 | 0.2 | 84.1 | 33.3 | 52.5 | 0 | 76.3 | 13.1 |
VarScan | 25.5 | 0 | 62.7 | 0 | 26 | 0 | 63 | 0 | 26.9 | 0 | 63.4 | 0 | 25.7 | 0 | 62.8 | 0.1 |
GATK | 99.6 | 1.5 | 99.1 | 99.1 | 97 | 0.7 | 98.1 | 92.6 | 88.4 | 0.5 | 93.9 | 72.9 | 72.9 | 0.4 | 86.2 | 42.7 |
16 Pooled Samples | %Sen | %FP | %BA | %SD | %Sen | %FP | %BA | %SD | %Sen | %FP | %BA | %SD | %Sen | %FP | %BA | %SD |
100 % Sample Covg | 50 % Sample Covg | 25 % Sample Covg | 12.5 % Sample Covg | |||||||||||||
CRISP | 99.1 | 4.2 | 97.4 | 98.1 | 91.2 | 4 | 93.6 | 81.5 | 74.2 | 3.5 | 85.3 | 48.3 | 57.3 | 3.3 | 77 | 24.5 |
SNVer | 61.3 | 4.4 | 78.4 | 27.8 | 47.6 | 3.3 | 72.1 | 9.8 | 36.1 | 1.6 | 67.3 | 1.7 | 27.3 | 0.9 | 63.2 | 0.3 |
LoFreq | 91.8 | 0.6 | 95.6 | 80.8 | 78.9 | 0.2 | 89.3 | 50.3 | 63.2 | 0.1 | 81.5 | 22.4 | 49.2 | 0.2 | 74.5 | 7.4 |
VarScan | 14.9 | 0 | 57.4 | 0 | 15.1 | 0 | 57.6 | 0 | 15.3 | 0 | 57.6 | 0 | 15.6 | 0 | 57.8 | 0 |
GATK | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |