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.
This method is described to be the "First pass of the base quality score recalibration". What is the second pass? It is not mentioned anywhere, or am I looking in the wrong place? In v1.2 there were two steps, is there only one step now for bqsr?