Gatk unified genotyper will take a bam/Sam and generate a vcf.

Sent from my iPhone

On Nov 8, 2011, at 6:54 AM, "David Matthews" 
<d.a.matth...@bristol.ac.uk<mailto:d.a.matth...@bristol.ac.uk>> wrote:

Hi,

Yes, I see that you can generate the VCF files that way but there is no 
seamless way of doing it entirely from within galaxy - i.e. you need to come 
out of galaxy at some point (or am I missing something?).


Best Wishes,
David.

__________________________________
Dr David A. Matthews

Senior Lecturer in Virology
Room E49
Department of Cellular and Molecular Medicine,
School of Medical Sciences
University Walk,
University of Bristol
Bristol.
BS8 1TD
U.K.

Tel. +44 117 3312058
Fax. +44 117 3312091

d.a.matth...@bristol.ac.uk<mailto:d.a.matth...@bristol.ac.uk>






On 8 Nov 2011, at 14:39, Chorny, Ilya wrote:

I got it working just fine on my local server. Could you expand on your vcf 
issue? I generate the vcf using gatk.

Sent from my iPhone

On Nov 8, 2011, at 6:36 AM, "David Matthews" 
<d.a.matth...@bristol.ac.uk<mailto:d.a.matth...@bristol.ac.uk><mailto:d.a.matth...@bristol.ac.uk>>
 wrote:

Hi,

I've had a few email chats with the author of snpEff and the fly in the 
ointment from my perspective is getting the vcf files it needs through Galaxy. 
As I understand it there is no way currently of getting the BAM/SAM files into 
the right input format so snpEff can use it within a Galaxy setup. So, whatever 
you do you'll still need one or two command line steps. We have a copy of 
snpEff here at Bristol on our Galaxy and when we did that we then realised 
there was no Galaxy method (that we could think of) for getting the input file 
ready for snpEFF to use. This is a pity as its actually a very nice piece of 
software with a nice professional looking output.

Best Wishes,
David.

__________________________________
Dr David A. Matthews

Senior Lecturer in Virology
Room E49
Department of Cellular and Molecular Medicine,
School of Medical Sciences
University Walk,
University of Bristol
Bristol.
BS8 1TD
U.K.

Tel. +44 117 3312058
Fax. +44 117 3312091

d.a.matth...@bristol.ac.uk<mailto:d.a.matth...@bristol.ac.uk><mailto:d.a.matth...@bristol.ac.uk>






On 8 Nov 2011, at 13:55, Dannon Baker wrote:

Hi Laura,

While the SNPeff developers have made Galaxy wrappers available, this is not a 
tool we currently have installed for use on the Galaxy server at 
main.g2.bx.psu.edu.  Off the top of my head, I don't know of any other public 
Galaxy servers that offer this tool, but if you have access to a local or cloud 
galaxy server you could use the provided wrapper to install the tool for use 
there.

Thanks!

-Dannon



On Nov 8, 2011, at 6:40 AM, Laura Elizabeth Spoor wrote:

Hi,

I use the Galaxy server and was wondering how to use SNPeff tool? I have seen 
that it can be integrating with Galaxy on their website 
(http://snpeff.sourceforge.net/images/snpEff_galaxy.png) but cannot see it on 
the server? Is it something that can be run on the server?

Best Wishes,

Laura

--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.


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