Question: Re: Snp Calling Problems (Jennifer Jackson)
gravatar for garzetti
5.2 years ago by
garzetti100 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 -- Debora Garzetti, PhD Student AG Rakin Max von Pettenkofer-Institute, LMU Pettenkoferstraße 9A 80336 Munich E-mail: Phone: +49 (0)89 2180 72915
galaxy • 911 views
ADD COMMENTlink modified 5.2 years ago by Jennifer Hillman Jackson25k • written 5.2 years ago by garzetti100
gravatar for Jennifer Hillman Jackson
5.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:
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: 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: Hopefully this helps to clarify, Jen Galaxy team -- Jennifer Hillman-Jackson
ADD COMMENTlink written 5.2 years ago by Jennifer Hillman Jackson25k
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