I was wondering if -newQual the default behavior in GATK 3.8 HaplotypeCaller? I receive an error that the argument is not available when I try to run HaplotypeCaller with GATK 3.8.
Never mind! By mistake, I was running an older version of GATK that I had on my system.
Though I have the same question, some months later. It looks like -new-qual (not the older syntax of -newQual) is still available, but still not the default, according to the 126.96.36.199 docs. Have people found problems with it that have prevented it from being the default, or is it just inertia? Apologies if I'm missing something in my searches. If so, at least this is a bump and not a whole new post.
The newQual is not yet the default in the latest GATK4 version, but it is very close to being the default. The team is doing some finalizing checks which you can keep track of here.