Re: [galaxy-user] SNP calling problems (Jennifer Jackson)
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-no...
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