Skip to main content

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.
Back to article page

BMC Genomics

ISSN: 1471-2164

Contact us