The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
Why are measured base insertion and deletion qualities only Q45 for BaseRecalibrator?
The measured qualities of the BI and BD are 45 in for this library. Normally I have a wide range for I and D qualities from 39-61. I have tried setting -ddq and -idq to -1, but that doesn't change anything. I am using dbsnp137 for my knowns, and otherwise just use default settings.