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I'm getting the following error in Haplotype Caller (2.8-1):
argument --defaultBaseQualities has value -1.00, but minimum allowed value is 0.0
while according to the CommandLine documentation the default value should be -1.
I'm running GATK through Galaxy, where all the inherited arguments (including --defaultBaseQualities) and their default values are common to all the tools, and I only received this error with HaplotypeCaller.