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.

gatk 4.05 and "fix_misencoded_quality_scores"

Switching from gatk 3.8 to 4.05 to avail myself of '--enotype-filtered-alleles' I discovered a few format changes to familiar options.

But '--fix_misencoded_quality_scores' is no longer recognized.

My question is what does HC (gatk 4) do when it encounters the problems that were previously handled with the '--fix_misencoded_quality_scores' option?



  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    Hi @chlangley,

    As you note, the on-the-fly option to fix misencoded qualities is no longer available in GATK4. We now have a stand-alone tool to fix misencoded quality scores called FixMisencodedBaseQualityReads. So you can preprocess your read file with this tool.

    Remember for GATK4, the parameters no longer use underscores _ but use dashes - and all lowercase letters.

    For anyone else landing on this page, misencoded quality scores are explained by this article.

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