Hi Mike,

Apologies for the delay in reply, your message was threaded under an announcement (perhaps accidentally sent as a reply to that thread?).


For GATK, we are not offering support yet as the pipeline is still considered beta. Most tool that are only on Test, and not on Main, are considered to be the same. That said, I can let you know that the tool is under active development, may change at any time, and comments about the current implementation is welcomed at galaxy development list.

http://wiki.g2.bx.psu.edu/Support#Unexpected_scientific_result

Take care,

Jen
Galaxy team


On 11/15/11 12:31 PM, Mike Dufault wrote:
Hello all,
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.
Thanks,
Mike



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___________________________________________________________
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