Question: Re: Snp Calling Problems (Jennifer Jackson)
0
garzetti • 100 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: garzetti@mvp.uni-muenchen.de
Phone: +49 (0)89 2180 72915
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modified 5.2 years ago
by
Jennifer Hillman Jackson ♦ 25k
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written
5.2 years ago by
garzetti • 100
