Question: Need help with "ANNOVAR Annotate VCF" tool
gravatar for tnc25
4.3 years ago by
United States
tnc2510 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 URL:


annovar-annotate-vcf • 2.8k views
ADD COMMENTlink modified 4.0 years ago by BrunoBSouzaa0 • written 4.3 years ago by tnc2510
gravatar for Jennifer Hillman Jackson
4.3 years ago by
United States
Jennifer Hillman Jackson25k wrote:


You are executing the tool on the public Main Galaxy instance at 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:

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

Hopefully one of these options will work out for you, Jen, Galaxy team

ADD COMMENTlink written 4.3 years ago by Jennifer Hillman Jackson25k
gravatar for BrunoBSouzaa
4.0 years ago by
BrunoBSouzaa0 wrote:

How do I input gene annotation file? I've downloaded it from gene ontology page but I can't use it on the input box!!

ADD COMMENTlink written 4.0 years ago by BrunoBSouzaa0

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 REPLYlink written 4.0 years ago by Martin Čech ♦♦ 4.9k
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