Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Errors about misencoded quality scores Follow

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    Peter Flanagan



    I use a program called MTBseq to analysis sequences of mycobacteria. The error I got was this;


    ERROR MESSAGE: SAM/BAM/CRAM file htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter@e584b2b appears to be using the wrong encoding for quality scores: we encountered an extremely high quality score of 66. Please see for more details and options related to this error.


    After looking above I assume I add those commands to my script as follows? Im not command line savvy and very much a novice. I run MTBseq on a cluster and use slurm sbatch to run. Can I just add the lines above to my scrip as shown below?








    SLURM Commands

    #SBATCH --partition=ProdQ
    #SBATCH --nodes=1
    #SBATCH --time=24:00:00
    #SBATCH --job-name=C10
    #SBATCH --account=ndlif075c
    #SBATCH --output=TBfull_Log.txt

    ##SBATCH --mail-user=xxxxxxxxxxxxxxxx
    ##SBATCH --mail-type=BEGIN,END


    load the environment module

    module load conda/2

    load the conda environment

    source activate MTBseq

    BASH Commands

    MTBseq --step TBfull --distance 5 --fix_misencoded_quality_scores -fixMisencodedQuals --threads 8

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