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Question: Need help with "ANNOVAR Annotate VCF" tool
1
gravatar for tnc25
4.3 years ago by
tnc25 • 10
United States
tnc25 • 10 wrote:

Hi!  I entered a vcf file into the annovar tool.  It looks like it ran and tells me then number of SNPs it found, but it gives me no output file.  All I entered for input was the vcf file.  

Thank you for your help.

Tool name: ANNOVAR Annotate VCF
Tool version: 0.1
Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/table_annovar/table_annovar/0.1
ToolShed URL: https://toolshed.g2.bx.psu.edu/view/devteam/table_annovar

 
annovar-annotate-vcf • 2.8k views
ADD COMMENT • link •
modified 4.0 years ago by BrunoBSouzaa • 0 • written 4.3 years ago by tnc25 • 10
0
gravatar for Jennifer Hillman Jackson
4.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

You are executing the tool on the public Main Galaxy instance at http://usegalaxy.org? If so, then the input VCF must be based on the hg19 reference annotation database and labeled as such to access additional annotation. Indexed reference annotation options appear in the tool form's "Annotation" boxes, where one or more can be selected to be incorporated into the run.

To run this tool with other reference genomes, please use the version in the Tool Shed with a cloud or local Galaxy. Instructions to get started are here:
http://usegalaxy.org/cloud
http://usegalaxy.org/toolshed

Other public instances may host this tool for certain genomes. These change frequently and a list of potential sites can be reviewed here:
http://wiki.galaxyproject.org/PublicGalaxyServers

Hopefully one of these options will work out for you, Jen, Galaxy team
ADD COMMENT • link written 4.3 years ago by Jennifer Hillman Jackson ♦ 25k
0
gravatar for BrunoBSouzaa
4.0 years ago by
BrunoBSouzaa • 0
Brazil
BrunoBSouzaa • 0 wrote:

How do I input gene annotation file? I've downloaded it from gene ontology page http://geneontology.org/page/download-annotations but I can't use it on the input box!!
ADD COMMENT • link written 4.0 years ago by BrunoBSouzaa • 0

Please create a new post with your question on this forum. Revival of an old and already answered post will only make things confusing to anybody who might answer your problem. Thanks

ADD REPLY • link written 4.0 years ago by Martin Čech ♦♦ 4.9k
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