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:
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies

The GATK forum has some discussion on the topic:
http://gatkforums.broadinstitute.org/discussion/1214/can-i-use-gatk-on-non-diploid-organisms

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:
usegalaxy.org/toolshed

Hopefully this helps to clarify,

Jen
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!
Debora

--
Jennifer Hillman-Jackson
http://galaxyproject.org

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