I have a sample in my .BAM file which has phred score ranging from 1-66. The quality score distribution looks like there are two scoring system (phred 33 and 64 ) mixed when someone did alignment earlier.
I was wondering how this might have happened? Anyway of processing the BAM files to bring it down to phred 33 scoring system ?
Note: I have used --fix_misencoded_quality_scores -fixMisencodedQuals in GATK but this just subtracts 31 which makes my quality score negative.
Thank You very much