Do I need to correct my base qualities or not?
I have recently upgraded to GATK v 2.4-9-g532efad and am implementing a pipeline for indel-realignment and base-quality recalibration. I decided to use the -fixMisencodedQuals flag in RealignerTargetCreator but am getting the following error.
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
This implies that the qualities need to be fixed and there is no solution in GATK.
However, if I simply remove the -fixMisencodedQuals flag from my call, then the bam files proceed without any error! So I'm a little confused about whether they need to be corrected or not? Are they valid for analysis?