A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
This utility makes it easy to convert between base quality values encoded in ASCII (as recorded in a FASTQ or SAM file) and their integer values representing the Phred-scaled probability that each base call is correct (as explained here).
See the FASTQ format documentation for more details on encoding scales.