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BAM problem prevents a fix_misencoded_quality_scores step

I ran the following code:
java -Xmx100g -jar /work/reecygroup/GATK/GenomeAnalysisTK.jar \
-T BaseRecalibrator --unsafe -nct 16 \
-R /work/reecygroup/index/bos_taurus/bos_taurus_all_dna.fa \
-I 2005-5105.realigned.bam \
-knownSites /work/reecygroup/christine/Bos_taurus.dbSNP.vcf \
-o 2005-5105.realigned.grp \

and got the error:

Bad input: while fixing mis-encoded base qualities we encountered a read that was correctly encoded; we cannot handle such a mixture of reads so unfortunately the BAM must be fixed with some other tool

The "index" and "knownSites" files have been successfully used in other run for quite some time, and the input BAM file (2005-5105.realigned.bam) was generated with a previous GATK IndelRealigner step. I wonder what could be wrong and what I need to do in order to fix it?


  • SheilaSheila Broad InstituteMember, Broadie admin


    Have a look at this thread. If you do a search for this error, it has been discussed in other threads as well.


  • zhilianghuzhilianghu IowaMember

    Sheila - Thank you! I was able to learn the cause (by IUPAC codes), and was able to proceed by omitting the "-fixMisencodedQuals" or "fix_misencoded_quality_scores" options (Previously I searched/found the thread and only to learn the alternative options ("-fixMisencodedQuals" vs. "fix_misencoded_quality_scores"). Not quite sure what negative impact by completely omitting this option. I have yet to try using fastqc/seqtk to fix the seqs. Again, many THANKS!

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