Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

Options -S LENIENT --fix_misencoded_quality_scores in RealignerTargetCreator and IndelRealigner

gsonggsong Posts: 3Member

Hi, I got errors when ran GATK RealignerTargetCreator and IndelRealigner in v2.4.9. I've checked many related discussions and comments. First, I got an error like "we encountered an extremely high quality score of 69" with option -S LENIENT and the GATK program stalled. So I added "--fix_misencoded_quality_scores", and then I got different error message "ERROR MESSAGE: Bad input: We encountered a non-standard non-IUPAC base in the provided reference: '0'" now. I tried older versions of GATK and both java 1.6 and 1.7. I'm hoping that you can help this. Please let me know if I'm missing something. Thanks!

--Giltae

Giltae Song, Ph.D. Postdoctoral researcher Department of Genetics School of Medicine Stanford

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  • gsonggsong Posts: 3Member

    Thanks for your note. I'm using sacCer3 in the UCSC genome browser in fasta format. It's Yeast reference genome and the file is not compressed.

    Giltae Song, Ph.D. Postdoctoral researcher Department of Genetics School of Medicine Stanford

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 5,293Administrator, GSA Member admin

    We've seen similar errors when people run GATK on Windows. Any chance you're on a Windows platform, or your reference file comes from a Windows filesystem?

    Geraldine Van der Auwera, PhD

  • gsonggsong Posts: 3Member

    I'm running on a linux machine with kernel version 2.6.32-279.5.1.el6.x86_64. I downloaded the reference file from the UCSC genome browser and it is a typical text file in FASTA. When I open it using 'vi', it looks fine.

    When I ran an older version of GATK (2.1.8) with other data with no --fix_misencoded_quality_scores using the same reference file, I got results successfully.

    Giltae Song, Ph.D. Postdoctoral researcher Department of Genetics School of Medicine Stanford

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 5,293Administrator, GSA Member admin

    OK, we'll look into this. In the meantime you can use the -XL argument to skip any positions where this occurs. Let me know if it happens at more than one.

    Geraldine Van der Auwera, PhD

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