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fixmisencoded quality scores for combination of correct and incorrect encoding

max_shpakmax_shpak Austin TXMember

When I rand Mutect on a .bam file for tumor and normal sequences, I received an error message about incorrectly encoded quality scores, so I applied the --fixencodedqualityscores and re-ran Mutect. This time, I'm getting an error message:

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

Evidently, this is because one of the files (control) was correctly encoded while the other (tumor, which I had to realign) was not. Is there a flag I can use to tell Mutect to only apply the quality scores fix to one of the files while running? Otherwise, there is an entire set of control .bams that I'll need to realign just to correct this problem.

Best Answer


  • SheilaSheila Broad InstituteMember, Broadie admin


    I don't think there is a flag in MuTect2 to do what you are asking. You can run PrintReads with the --fixencodedqualityscores flag on just the tumor BAM to fix the quality scores. However, did you follow the Best Practices pre-processing steps? If you did, you should not be running into this error at this step.


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