Hi Debora,

This option was introduced in a version of GATK that is newer than the one on the public Main Galaxy server under the tool group "NGS: GATK Tools (beta)". The version of tools running here is "GATK (1.4)"

This is noted here for reference and in the tool output:

The GATK forum has some discussion on the topic:

The newer version of GATK has not been wrapped for Galaxy. But if this was something you or someone else reading this post did, the Tool Shed would be a great place to share it:

Hopefully this helps to clarify,

Galaxy team

On 10/1/13 1:48 AM, garzetti wrote:
Hi Jen,

thank you for your answer!

I have used the Add or Replace group tool and it worked pretty well, so that I could use the FreeBayes tool with no problem!

Now I have another question: I have been pre-processing my data with the NGS: GATK tools according to their Best Practices and I am ready for SNP calling. I have read the Unified Genotyper documentation and, since I am working with bacterial genome sequences, I would need to set the -sample-ploidy argument to 1 (default 2). I cannot find this option in the Galaxy version of this tool, not even in the advanced options. How can I do that?

Thank you very much!

Jennifer Hillman-Jackson

The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:


To manage your subscriptions to this and other Galaxy lists,
please use the interface at:


To search Galaxy mailing lists use the unified search at:


Reply via email to