Gatk unified genotyper will take a bam/Sam and generate a vcf.
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On Nov 8, 2011, at 6:54 AM, "David Matthews"
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
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
Senio
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"
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
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 s
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
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,
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