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_GAT... 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:dan@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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