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Table 1 Comparison of indel calling in the 6 training samples using different variant calling workflows, without subsequent filtering

From: Evaluation and optimisation of indel detection workflows for ion torrent sequencing of the BRCA1 and BRCA2 genes

Read mapper Variant caller FPa FNa TPa TNa Sensitivity [95% CI] Specificity [95% CI] FDR [95% CI]
TMAP-TS2.0 TSVC2.0 0 2 1 96135 33.33% [3.87, 82.33] 100% [100, 100] 0% [0, 77.15]
TMAP-TS2.2 TSVC2.2 0 2 1 96135 33.33% [3.87, 82.33] 100% [100, 100] 0% [0, 77.15]
TMAP-TS3.4 TSVC3.4 8 1 2 96127 66.67% [17.67, 96.13] 99.99% [99.98, 100] 80% [49.72, 95.59]
TMAP-TS2.0 GATK 4 1 2 96131 66.67% [17.67, 96.13] 99.99% [99.99, 100] 66.67% [28.64, 92.32]
TMAP-TS2.2 GATK 9 1 2 96126 66.67% [17.67, 96.13] 99.99% [99.98, 100] 81.82% [53.28, 96.02]
*TMAP-TS3.4 GATK 5 0 3 96130 100% [55.59, 100] 99.99% [99.99, 100] 62.5% [29.48, 88.1]
TMAP-TS2.0 SAMtools 0 3 0 96135 100% [55.59, 100] 99.97% [99.96, 99.98] 90.62% [77.05, 97.29]
TMAP-TS2.2 SAMtools 39 3 0 96096 100% [55.59, 100] 99.99% [99.98, 99.99] 81.25% [57.92, 94.42]
*TMAP-TS3.4 SAMtools 17 0 3 96118 100% [55.59, 100] 99.98% [99.97, 99.99] 85% [65.14, 95.59]
*BWA GATK 1 0 3 96134 100% [55.59, 100] 99.99% [99.99, 100] 25% [2.85, 71.62]
*BWA SAMtools 20 0 3 96115 100% [55.59, 100] 99.98% [99.97, 99.99] 86.96% [69.13, 96.19]
  1. We considered all bases in coding exons. Across the 6 samples the total number of bases considered was 96,138.
  2. aFP = False Positives; FN = False Negatives; TP = True Positive; TN = True Negatives.
  3. *Workflow with 100% sensitivity.