Question: GATK 2.8 reference genome and "data_manager_gatk_picard_index_builder"
0
gravatar for christophe.habib
3.2 years ago by
France
christophe.habib340 wrote:

Hi everyone,

Now that I succeeded on installing GATK2.8, and I am trying to use it. According to the form I need to set a reference genome but I have no options available.. I supposed that the data_manager_gatk_picard_index_builder purpose was to do it properly without writing directly in the loc file by myself.

Am I wrong? I wonder if I have to write in the loc file, and in this case, what is the purpose of this data manager?

Thank you

Christ

reference genome gatk • 712 views
ADD COMMENTlink modified 3.2 years ago by Jennifer Hillman Jackson25k • written 3.2 years ago by christophe.habib340
0
gravatar for Jennifer Hillman Jackson
3.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

You could just install a reference genome (that was GATK-sorted, see their web site and manual about how to do). This would provide a reference genome but none of the extra files.

Or you can obtain all of the data from the binary package from the GATK source and install it line-command. The same is true for certain other tool suites with reference data that is more complex than just a genome.

The Data Manager you point out is just one part of setting up the data. We welcome Data Manager contributions to the Tool Shed

More about organizing data is in the Galaxy wiki here, including the location of our rsync server. That server is a good way to see how data is put together for http://usegalaxy.org.
https://wiki.galaxyproject.org/Admin/DataIntegration

Using a Custom reference genome is also a choice, please see:
https://wiki.galaxyproject.org/Support#Tools_on_the_Main_server:_GATK

Best, Jen, Galaxy team

ADD COMMENTlink written 3.2 years ago by Jennifer Hillman Jackson25k
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