I am trying to run through the GATK pipeline on the Galaxy Test page. I have a
question related to the UnifiedGenotyper wrapper page. At the bottom of the
page, I choose the
"Advanced" tab for "Basic or Advanced Analysis options."
After the automatically refreshed, I choose the "Annotation Types" that I was
interested in. Then below that are options for "Annotation Interfaces/Groups:"
What are these options used for? I have looked all over the web, on the GATK
wiki and at the GATK Q&A page (located at getsatisaction.com) without any luck.
Are these options important?
The description located at the bottom of the page lists: Group - One or more
classes/groups of annotations to apply to variant calls.
What type of group or class is "Standard", "Experiments" or "WorkInProgress?"
Does "class" refer to a Java "class" in a similar way that annotations are
"arguments?" Any clarification would be very helpful.
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