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Question: Need help with "SnpEff" tool
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gravatar for 11011560-068
3.8 years ago by
11011560-068 • 0
Pakistan
11011560-068 • 0 wrote:

hi i am trying to use snpeff on galaxy...i give vcf file but i dnt know in genome portion what i have to select in two options ...can anyone help me

 Tool name: SnpEff

Tool version: 1.0
Tool ID: toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/snpEff/1.0
ToolShed URL: https://toolshed.g2.bx.psu.edu/view/pcingola/snpeff

 
snpeff • 987 views
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modified 3.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.8 years ago by 11011560-068 • 0

Hi, please try to reformulate your question and be precise. Which options, what do you want to do etc ... We will try to help you :)

ADD REPLY • link written 3.8 years ago by Bjoern Gruening ♦ 5.1k
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gravatar for Jennifer Hillman Jackson
3.8 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

If your data is not based on one of the two reference genomes listed on the tool form, then the SnpEff tool is not available for use on the public Main Galaxy instance. You will need to obtain the tool from the tool shed, add it to a local/cloud Galaxy, and use it there. 

http://usegalaxy.org/toolshed 
https://wiki.galaxyproject.org/BigPicture/Choices

Best, Jen, Galaxy team
ADD COMMENT • link written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k
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