Question: Need help with "ANNOVAR Annotate VCF" tool
0
gravatar for mariano.avino
4.1 years ago by
European Union
mariano.avino0 wrote:

Hi there,

When I open Annovar annotate VCF tool on Galaxy I cannot visualize any option for the boxes Gene Annotations, Annotation Regions, and Annotation Databases. There is nothing for me to select, could you tell me how I can get some of those?

Thanks a lot,

Mariano


 

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

 

ADD COMMENTlink modified 4.0 years ago by Jennifer Hillman Jackson25k • written 4.1 years ago by mariano.avino0
0
gravatar for Jennifer Hillman Jackson
4.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hi Mariano,

This earlier post was about the same tool questions and I wrote up the full range of solution advice. Please see and let us know if you need more info:
Need help with "ANNOVAR Annotate VCF" tool

Best, Jen, Galaxy team

ADD COMMENTlink written 4.1 years ago by Jennifer Hillman Jackson25k

Thank you for your answer,

and regarding to that earlier post you sent me I had already aligned my file with hg19 however I had done all my analysis on my GATK shell which I installed on my machine, then I upload my vcf file on Galaxy just to run the ANNOVAR. Then I got the problem.

ADD REPLYlink written 4.1 years ago by mariano.avino0

My guess is that the "database" attribute needs to be set for your datasets. See here for how to do that: 
http://wiki.galaxyproject.org/Support#Tool_doesn.27t_recognize_dataset

 

ADD REPLYlink written 4.0 years ago by Jennifer Hillman Jackson25k
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