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

 
genome metadata vcf database annovar-annotate-vcf • 3.7k views
ADD COMMENT • link •
modified 4.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.2 years ago by mariano.avino • 0
0
gravatar for Jennifer Hillman Jackson
4.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 4.2 years ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link written 4.2 years ago by mariano.avino • 0

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 REPLY • link written 4.2 years ago by Jennifer Hillman Jackson ♦ 25k
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