There are now error-corrected NGS technologies that can produce base quality scores Q60+. To make those technologies compatible with the Manta program, we need to increase the maximum allowed base quality score. A score of 93 is the maximum defined in the SAM spec v1 §4.2.3:
Base qualities are stored as bytes in the range [0, 93], without any +33 conversion to printable ASCII.
There are now error-corrected NGS technologies that can produce base quality scores Q60+. To make those technologies compatible with the Manta program, we need to increase the maximum allowed base quality score. A score of 93 is the maximum defined in the SAM spec v1 §4.2.3:
This is also the maximum for the HTSJDK project.