I'm dealing with a new situation. Let's imagine I want to use the Indel Realigner from GATK on Galaxy.
Thing is, with my BAM file, I must enable the "-fixMisencodedQuals / --fix_misencoded_quality_scores" option in order no to make the run crash. This option is reachable by enabling the GATK advanced options. Unfortunately, this automatically activates every other parameters of GATK advanced options. For example: "-DBQ,--defaultBaseQualities ", "-baqGOP,--baqGapOpenPenalty " and so on.
And this gives me a different outcome, just because of these new parameters. In other words, is there a way to only set the "-fixMisencodedQuals / --fix_misencoded_quality_scores" option?
I'm really desperate here. I thank you for your Kindly,