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Hello dear GATK Team,
since Version 2.3 I get the following error with some Lifescope 2.5 mapped SoLID exome Bam files:
"[...]appears to be using the wrong encoding for quality scores: we encountered an extremely high quality score of 64; please see the GATK --help documentation for options related to this error".
After carefully seaching the forum I found this discussion:
where ebanks offered the "--allow_potentially_misencoded_quality_scores" argument as solution.
Actually this seemed to work at first, all walkers with the argument applied don't crash any more.
The Problem is that UnifiedGenotyper and HaplotypeCaller seem to somehow ignore the reads (or something else...) because in these exomes both call only about 3000 variants, allthough they seem to process the whole file judged by the runtime and logfiles.
The exomes used to work and had normal calls prior to GATK 2.3.
(the argument "--fix_misencoded_quality_scores" / "-fixMisencodedQuals"
as mentioned in this post: gatkforums.broadinstitute.org/discussion/1991/version-highlights-for-gatk-version-2-3
messes things up more for the Lifescope BAMs)