I've created a full Variant Calling pipeline (on Galaxy). There is of course the IndelRealignment phase done by GATK.
We all know now the solution of the "SAM/BAM file x appears to be using the wrong encoding for quality scores" problem by applying this option "--fix_misencoded_quality_scores" or not applying it.
My question is, can we ascertain if you need to apply this option or not before actually running the pipeline? For now I have been running the pipeline, and changing the option if it did fail, of course wasting time.
I thank you in advance for you help.