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

Table 3 Comparison of indel calling in the 17 additional test samples using different workflows with QD _th and VARW _th filters

Read mapper	Variant caller	QD_th	FP^a	TP^a	TN^a	Sensitivity [95% CI]	Specificity [95% CI]	FDR [95% CI]
TMAP-TS3.4	GATK	2.5	25	2	272364	100% [43.07, 100]	99.99% [99.99, 99.99]	92.59% [78.3, 98.43]
TMAP-TS3.4	SAMtools	1	2	2	272387	100% [43.07, 100]	99.99% [99.99, 100]	50% [12.28, 87.72]
BWA	GATK	2.5	14	2	272375	100% [43.07, 100]	99.99% [99.99, 100]	87.5% [65.58, 97.31]
BWA	SAMtools	1	4	2	272385	100% [43.07, 100]	99.99% [99.99, 100]	66.67% [28.64, 92.32]

We considered all bases in coding exons. Across the 17 samples the total number of bases considered was 272,391.
^aFP = False Positives; FN = False Negatives; TP = True Positive; TN = True Negatives.

ISSN: 1471-2164