Question: Enabling "GATK Advanced Options" on a tool impacts the run
gravatar for jgbaumann
10 months ago by
jgbaumann10 wrote:

Hello Everyone,

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,


ADD COMMENTlink modified 10 months ago by Jennifer Hillman Jackson25k • written 10 months ago by jgbaumann10
gravatar for Jennifer Hillman Jackson
10 months ago by
United States
Jennifer Hillman Jackson25k wrote:


GATK tools have been deprecated for a while now on public servers and the tool wrappers from the Tool Shed are not recommended for use in a local/docker/cloud Galaxy. There will be no future upgrades to GATK wrappers (as of this time, and likely ongoing).

Alternative tools/workflows for Variant analysis are covered in several tutorials here:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 10 months ago by Jennifer Hillman Jackson25k
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