Hi Xiaojing,

Data for hg17 is not yet available for this toolset. You may still be able to 
use this tool if you upload your own FASTA genome file. Please be sure to 
respect the GATK genome ordering rules and reorder your BAM file if necessary: 
http://www.broadinstitute.org/gsa/wiki/index.php/Preparing_the_essential_GATK_input_files:_the_reference_genome

However, because these tools are still under development/experimental we 
recommended that you remap your sequences against the "hg_g1k_v37" genome if 
you want to use these tools at this time.

Also, please keep all replies on the mailing list.

Thanks for using Galaxy,

Dan


On Aug 18, 2011, at 1:33 PM, Hong, Xiaojing wrote:

> Hi, Dan
>  
> I did set the genome build to HG17 but I still can’t see the select box.
>  
> Xiaojing Hong
> Ph.D candidate
> Department of Biology
> Manak Lab
> 455 Biology Building
> University of Iowa
> Iowa City, IA 52242
> (P) 319-335-0266
>  
> From: Daniel Blankenberg [mailto:d...@bx.psu.edu] 
> Sent: Thursday, August 18, 2011 12:19 PM
> To: Hong, Xiaojing
> Cc: galaxy-user@lists.bx.psu.edu
> Subject: Re: [galaxy-user] question about the GATK tools
>  
> Hi Xiaojing,
>  
> You'll need to make sure that the dbkey of your input BAM file is set to a 
> genome build that has data available. Click the pencil icon to set the genome 
> build.  If you have set the genome build, but still have an empty select box 
> then data may not be available for this build/tool combination, you can 
> request that the needed data be added for this tool. If your reference genome 
> is not available, you can also upload a FASTA file containing the genome and 
> access it directly from the history.
>  
>  
> Thanks for using Galaxy,
>  
> Dan
>  
>  
> On Aug 17, 2011, at 11:26 AM, Hong, Xiaojing wrote:
> 
> 
> Hi,
>  
> I just uploaded the BAM file for an exome sequencing sample and was trying to 
> use the GATK tools. In the first step, realigner Target creator, I can see my 
> uploaded file but I can’t see any options under the “using reference genome” 
> and the following choices so I can’t click execute. Did I do anything wrong? 
> Thanks!
>  
> Xiaojing Hong
> University of Iowa
> 
> 
>  
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___________________________________________________________
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