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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.