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Table 3 Comparison of indel calling in the 17 additional test 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 25 0 2 272364 100% [43.07, 100] 99.99% [99.99, 99.99] 92.59% [78.3, 98.43]
TMAP-TS3.4 SAMtools 1 0 2 0 2 272387 100% [43.07, 100] 99.99% [99.99, 100] 50% [12.28, 87.72]
BWA GATK 2.5 0 14 0 2 272375 100% [43.07, 100] 99.99% [99.99, 100] 87.5% [65.58, 97.31]
BWA SAMtools 1 0 4 0 2 272385 100% [43.07, 100] 99.99% [99.99, 100] 66.67% [28.64, 92.32]
  1. We considered all bases in coding exons. Across the 17 samples the total number of bases considered was 272,391.
  2. aFP = False Positives; FN = False Negatives; TP = True Positive; TN = True Negatives.