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Table 2 Effects of submitting multiple and individual pooled BAM files to each program

From: Evaluation of variant detection software for pooled next-generation sequence data

a
Group Size Sen% FP% BA% SD%
CRISP-2 pools 97.8 10.5 93.7 95.3
CRISP-4 pools 96.1 7.5 94.3 91.6
CRISP-8 pools 97.2 7.4 94.9 94.1
SNVer-1 pool 72.4 3.3 84.6 52.9
SNVer-2 pools 71.4 3.3 84.1 51
SNVer-4 pools 70.4 3.3 83.6 49
SNVer-8 pools 69.4 3.2 83.1 47.1
VarScan-1 pool 29.3 0.1 64.6 0.1
VarScan-2 pools 29.3 0.1 64.6 0.1
VarScan-4 pools 29.3 0.1 64.6 0.1
VarScan-8 pools 29.2 0.1 64.5 0.1
GATK-1 pool 98.2 9.1 94.6 95.9
GATK-2 pools 98.2 9 94.6 95.8
GATK-4 pools 98.1 8.6 94.7 95.5
GATK-8 pools 98 8.5 94.7 95.1
b
Group Size Sen% FP% BA% SD%
CRISP-2 pools 97.1 4.1 96.5 93.2
CRISP-4 pools 92.2 4 94.1 83.4
SNVer-1 pool 74.4 1 86.7 53.6
SNVer-2 pools 73.7 1 86.3 52.5
SNVer-4 pools 72.8 1 85.9 50.8
VarScan-1 pool 41 0 70.5 3.1
VarScan-2 pools 41 0 70.5 3.1
VarScan-4 pools 40.9 0 70.5 3.1
GATK-1 pool 98 0.2 98.9 95.2
GATK-2 pools 97.9 0.2 98.9 95.1
GATK-4 pools 97.9 0.2 98.9 95
  1. In (a), all values were calculated using eight ClinSeq samples per pool with 35.1x average total coverage (50 % of typical full coverage for each sample). In (b), all values were calculated using four Thousand Genomes samples per pool with 21.0x average total coverage (50 % of typical full coverage for each sample)
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