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tgen / pegasusPipe

MIT License
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recalibration fails because of quality score #19

Open tgenahmet opened 7 years ago

tgenahmet commented 7 years ago

GATK fails because of

"##### 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.

tgenahmet commented 7 years ago

Testing this on: NMTRC_C018_0050_ps201703031540