Entering edit mode
10.2 years ago
venks
▴
740
Hi,
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
That's a first. Both SAM and BAM files should only ever have Phred+33, so I wonder how this was made. Do you know anything about that?
Ryan,
Thanks for the reply.
The data is pretty old. It came from SOLID sequencing. It was later aligned using Novoalign.
Nothing says fun like trying to make sense of old data :(
I am having the same problem in this moment, did you manage to solve it? If yes, how?