Table 3.
Benchmarked values from variant calling software analysis.
| Sample | SRA accession | Software/platform | Variant caller | SNV precision | SNV recall | SNV F1 | SNV non-assessed | Indel precision | Indel recall | Indel F1 | Indel non-assessed | Average run time (min) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HG001 | ERR1905890 | Illumina | DRAGEN | 99.87% | 99.72% | 99.80% | 8.77% | 97.92% | 97.65% | 97.79% | 26.96% | 35.81 |
| CLC | Unknown | 98.74% | 99.23% | 98.99% | 9.94% | 88.19% | 91.56% | 89.84% | 27.83% | 25.63 | ||
| Partek | GATK | 97.86% | 99.23% | 98.54% | 10.97% | 85.79% | 94.70% | 90.03% | 30.37% | 1,782.05 | ||
| Freebayes + Samtools | 96.23% | 99.22% | 97.70% | 10.88% | 69.05% | 92.70% | 79.15% | 24.95% | 769.13 | |||
| Varsome | GATK | 98.58% | 99.20% | 98.89% | 11.46% | 93.29% | 94.85% | 94.07% | 28.32% | 183.67 | ||
| HG002 | SRR2962669 | Illumina | DRAGEN | 99.87% | 99.33% | 99.60% | 6.97% | 97.27% | 96.15% | 96.71% | 19.89% | 29.21 |
| CLC | Unknown | 98.65% | 98.83% | 98.74% | 8.02% | 91.92% | 92.06% | 91.99% | 19.98% | 7.32 | ||
| Partek | GATK | 97.92% | 98.86% | 98.39% | 8.74% | 87.14% | 93.61% | 90.26% | 21.59% | 247.80 | ||
| Freebayes +Samtools | 96.49% | 98.84% | 97.65% | 8.71% | 56.89% | 91.44% | 70.14% | 16.50% | 347.56 | |||
| Varsome | GATK | 98.10% | 98.56% | 98.33% | 8.90% | 94.65% | 91.85% | 93.23% | 19.21% | 116.67 | ||
| HG003 | SRR2962692 | Illumina | DRAGEN | 99.92% | 99.41% | 99.66% | 7.82% | 96.54% | 96.41% | 96.47% | 23.24% | 28.51 |
| CLC | Unknown | 98.54% | 98.92% | 98.73% | 8.65% | 91.82% | 93.12% | 92.46% | 22.57% | 6.25 | ||
| Partek | GATK | 97.80% | 98.84% | 98.32% | 9.99% | 84.67% | 92.86% | 88.57% | 24.43% | 218.12 | ||
| Freebayes + Samtools | 96.34% | 98.89% | 97.60% | 9.43% | 55.45% | 91.47% | 69.05% | 19.50% | 314.43 | |||
| Varsome | GATK | 97.98% | 98.42% | 98.20% | 10.00% | 94.13% | 90.48% | 92.27% | 22.55% | 111.00 |
SNV, single nucleotide variant; Indel, insertion or deletion; F1, harmonic mean.