The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!
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?