Tool for calibrating base quality scores?
I think what you are looking for is GATK's Base Quality Score Recalibration.  Their documentation is great so I won't rewrite it here.  


  BQSR stands for Base Quality Score Recalibration. In a nutshell, it is
  a data pre-processing step that detects systematic errors made by the
  sequencing machine when it estimates the accuracy of each base call.