Table 2.

Comparison of the area under the ROC curve (AUC)

	Original	ReQON	GATK	BAQ
Replicate 1	0.673	0.806	0.824	0.798
Replicate 2	0.764	0.881	0.874	0.814

Comparison of AUC for two cell line replicates recalibrated with ReQON, GATK and BAQ. Bases from chromosome 20 that do not match the reference sequence are separated as belonging to positions in dbSNP version 132 or not. Overall, all three recalibration methods outperform the original quality scores. ReQON and GATK have similar AUC values, with both methods outperforming BAQ.