Tool for calibrating base quality scores? A given sequencing machine assigns a 'certainty' to each base call in the form of a per-base quality score (FASTQ format).

I have reads from several machines aligned to the corresponding reference (BAM format or similar). Ignoring SNPs and misalignments (for simplicity), mismatches should represent sequencing errors.

I'd like to parse through the FASTQ and BAM file and evaluate how closely the per-base quality score reflects 'true' sequencing errors.

Is there an existing efficient, user-friendly, open source, well documented tool to do this? Failing that, is there a paper doing this that claims to have made the tool freely available?

Another method would be to look at bases corrected using kmer analysis or similar. Again, the per-base quality score can be compared to the 'true' sequencing errors.

Any tool to do that? I guess it could be baked into an existing error correction tool.

Do short read aligners actually make use of per-base quality score?

Many thanks,
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.