--defaultBaseQualities in Haplotype caller
Posted in Ask the GATK team | Last updated on

Comments (3)

Dear Team, 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.

Regards, Paolo Uva

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