GATK error: appears to be using the wrong encoding for quality scores: we encountered an extremely high quality score of \d+

When looking at the GATK forums, it looks like there are at least 2 likely solutions:

1) Add "--fix_misencoded_quality_scores -fixMisencodedQuals" to the commands (see http://gatkforums.broadinstitute.org/discussion/1991/version-highlights-for-gatk-version-2-3)

2) Add "-allowPotentiallyMisencodedQuals" to the commands (see http://gatkforums.broadinstitute.org/discussion/2500/depthofcoverage-producing-extremely-high-quality-score-error or http://gatkforums.broadinstitute.org/discussion/2335/realignment-with-high-base-qualities)

Cited from https://www.biostars.org/p/94637/