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Table 2 Comparison of indel calling in the 6 training samples using different workflows with QD th and VARW th filters

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

Read mapper Variant caller QDth VARWth FPa FNa TPa TNa Sensitivity [95% CI] Specificity [95% CI] FDR [95% CI]
TMAP-TS3.4 GATK 2.5 0 1 0 3 96134 100% [55.59, 100] 99.99% [99.99, 100] 25% [2.85, 71.62]
TMAP-TS3.4 SAMtools 1 0 0 0 3 96135 100% [55.59, 100] 100% [100, 100] 0% [0, 44.41]
BWA GATK 2.5 0 0 0 3 96135 100% [55.59, 100] 100% [100, 100] 0% [0, 44.41]
BWA SAMtools 1 0 0 0 3 96135 100% [55.59, 100] 100% [100, 100] 0% [0, 44.41]
  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.