Table 1

Comparison of Frequency-Weighted Squared Error (FWSE)
Original ReQON GATK BAQ
Chromosome 10 Replicate 1 69.36 3.61 11.55 13.93
Replicate 2 62.89 5.31 14.91 21.76
Chromosome 20 Replicate 1 71.09 3.04 12.28 15.93
Replicate 2 64.34 5.82 17.43 24.38

Comparison of FWSE for two cell line replicates between original quality scores reported from the sequencer machine and after recalibration with ReQON, GATK and BAQ. ReQON quality scores have the lowest FWSE values, corresponding to increased accuracy. ReQON does not overfit the model to the training set, shown by the roughly equivalent FWSE values for both the training (chromosome 10) and testing (chromosome 20) sets after recalibration.

Cabanski et al.

Cabanski et al. BMC Bioinformatics 2012 13:221   doi:10.1186/1471-2105-13-221

Open Data