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-d...
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