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about argument presentation
I find it sometimes quite non-intuitive which to specify from
with some picard and or gatk commands.
Would it be possible to unify the way arguments are called and separated from their values and to include all valid alternates in the docs?
Is there already a preference for the future to which we should start to converge when we have the choice?
I have scripts that do not execute anymore with today's command versions which makes it painful sometimes.
Thanks in advance