"##### ERROR MESSAGE: SAM/BAM/CRAM file htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter@75830b41 appears to be using the wrong encoding for quality scores: we encountered an extremely high quality score of 62. Please see https://www.broadinstitute.org/gatk/guide?id=6470 for more details and options related to this error."
Looks like it can be fixed with: --fix_misencoded_quality_scores
@PedalheadPHX Can I add this option?
@denriquez this effects C018_0050.
GATK fails because of
Looks like it can be fixed with: --fix_misencoded_quality_scores @PedalheadPHX Can I add this option? @denriquez this effects C018_0050.