Hi Mathew,
Regarding 1 you might want to read this thread:
http://user.list.galaxyproject.org/Problem-with-Depth-of-Coverage-on-BAM-files-GATK-tools-td4654147.html
All tools from GATK are limited to hg_g1k_v37 as far as I know.
Best,
Carlos
On Mon, Aug 6, 2012 at 10:30 AM, Mathew Bunj
Hello Mathew,
Carlos is correct the the tools in the group NGS: GATK Tools (beta)
will require that the data is mapped/associated with the reference
genome hg_g1k_v37. Belinda has offered to help with the details that
go beyond Galaxy and that is great - the GATK forum is definitely the
best
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