Hi Sathya,
The SnpEff tool is set up at this time for annotation with the /C.
elegans/ WS220 genome only. Including human in the future on the public
Main server at http://usegalaxy.org is under current evaluation.
For now, use the tool in a local or cloud Galaxy instance, with the tool
Hello,
SNPEff is available for use with the human reference genome in the GATK
pipeline (the 1000 genomes version, called Homo sapiens b37
(hg_g1k_v37) in Galaxy). See the tool NGS: GATK Tools (beta) -
Variant Annotator and look in the list of Annotations to apply.
The best documentation is
Thanks John, Pablo,
Updates are of course welcomed in the Tool Shed. Thanks for letting the
Galaxy community aware that this may come up during analysis.
Best,
Jen
Galaxy team
On 12/13/11 12:17 PM, John David Osborne wrote:
Hi Pablo,
Correct me if I am wrong, but I believe that SNPEff
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
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.ukmailto:d.a.matth...@bristol.ac.uk wrote:
Hi,
I've had a few email chats with the author
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
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.ukmailto: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
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