Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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.