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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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