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Question: Running SnpEff on Galaxy
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gravatar for lrutter
4.0 years ago by
lrutter • 0
United States
lrutter • 0 wrote:

Hello,

I would like to annotate a .vcf file and also summarize possible effects variants can have on genes (stop codon, amino acid changes, etc.)

It seems that is what the output of SnpEff can provide (http://snpeff.sourceforge.net/SnpEff.html).

I have uploaded a .vcf file, .fasta file, and .gff3 file to Galaxy.

I try the program on the leftbar of Galaxy (SnpEff: Variant effect and annotation). For the "Sequence Changes" field, I put the .vcf file. For the "Input Format" field, I put VCF. For the "Genome" field, it seems there are only two hard-coded choices to choose from. My species is Seriola, which is not listed.

My question is: Do I have the necessary files in the necessary places to run SnpEff on Galaxy? If not, is there any tool on Galaxy that I can use to annotate .vcf file and summarize effects the variants can have on genes?

 

Thank you for any advice..!

 
snp galaxy • 2.9k views
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modified 4.0 years ago • written 4.0 years ago by lrutter • 0

I see... Thank you for your explanation, Jennifer.

ADD REPLY • link written 4.0 years ago by lrutter • 0
0
gravatar for Jennifer Hillman Jackson
4.0 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

When using the public Main Galaxy instance, only the listed genomes are available. In order to use more, start up a cloud instance of Galaxy, add the tool from the tool shed, and set up the reference data. The form does not support adding in custom reference data through the UI at this time. Amazon offers a grant program that can help with costs, they are very generous. Some other public instances support this tool for other genomes, but you'll need to look through the alternatives and review their latest supported content.

http://wiki.galaxyproject.org/BigPicture/Choices

http://usegalaxy.org/toolshed

Hopefully you will find a good alternative, Jen, Galaxy team
ADD COMMENT • link written 4.0 years ago by Jennifer Hillman Jackson ♦ 25k
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