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,
I would like to use SNPeff for annotation through GATK, However when I upload
my file it seems like I cannot use it for this task. My file is .txt and is in
this format :
Chr locationref allele alt allele
1 1234567A
Hi,
Is it possible to use SNPeff with genomes other than worm. This seems to be
the only option on the main Galaxy server.
Thanks,
David
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The Galaxy User list should be used for the discussion of
Galaxy analysis and other features
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
Hello Raj,
This tool is from the Tool Shed and is maintained by the tool author. To
contact them about functionality or problems, go to the Tool Shed at
http://toolshed.g2.bx.psu.edu/, locate the repository (search by
'snpEff'), click on the name, in the the top far right corner locate the
Hi All,
I updated galaxy recently to the latest version. Everything looks fine, except
snpEff report html view. It was displaying properly (all tables and summary
values) before the update, but the summary values are not displaying after the
update. A sample screen-shot is attached for your
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 Pablo,
Correct me if I am wrong, but I believe that SNPEff doesn't check the inserted
sequence when computing the effect of an insertion?
For instance an insertion of TTTA will be reported as a frameshift mutation. In
the majority of cases this is fine, however if the current reading frame
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,
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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