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

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

Read mapper	Variant caller	FP^a	FN^a	TP^a	TN^a	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]

We considered all bases in coding exons. Across the 6 samples the total number of bases considered was 96,138.
^aFP = False Positives; FN = False Negatives; TP = True Positive; TN = True Negatives.
*Workflow with 100% sensitivity.

ISSN: 1471-2164