Table 2. Sensitivity and false positive rates on the validation set.

	Academic PGM pipeline		NextGene pipeline (v2.3)
	Sensitivity	False-positive rate	Sensitivity	False-positive rate
Number of expected SNVs=66	98.5% (65 detected)	1.5% (1 false positive)	100% (66 detected)	0% (no false positives)
Number of expected indels=9	77.8% (7 detected)	30% (3 false positives)	100% (9 detected)	87.7% (64 false positives)

Sensitivity was calculated as follows: (number of true positives/(number of true positives+number of false negatives)). Specificity was estimated by the using the false-positive rate calculated as follows: (number of false positives/(number of false positives+number of true positives)), see text for details.