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quality score error
Hi I am using whole genome sequence data of sanger sequencing, and I am having the error:
we encountered an extremely high quality score of 68
One posible solution is to use the flag -allowPotentiallyMisencodedQuals
The only explanation about this flag that I found is: Ignore warnings about base quality score encoding, and is here https://wiki.gacrc.uga.edu/wiki/Gatk
Thus if I use this flag I can conserve this "High quality score" bases for the analysis and SNP calling? Because that is what I want.
Thank you very much