Variant Annotation In Galaxy

Question: Variant Annotation In Galaxy

4.8 years ago by

garzetti • 100

Germany

garzetti • 100 wrote:

Hallo Galaxy users, I would like to annotate variants (in vcf file) found in my bacterial genomes and look which of them cause non-synonymous mutations. I have found two tools in the Main Galaxy that I can use for this purpose (snpEff and Annovar), but I have problems with them. How can I change the input genome in snpEff? The only available choice in C. elegans. How can I choose my genome, already uploaded in my history? Regarding Annovar, which file formats are required as Gene annotations/ Annotation Regions/ Annotation Databases? Reading the tool manual, it seems I can create my own txt/tabular files and use them for annotation, but the tool in Galaxy doesn't allow me to select any file, even if I have txt files in my history. Any other suggested tool I can use? Thanks! Debora

snpeff snp • 3.9k views

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modified 4.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.8 years ago by garzetti • 100

4.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello Debora, There are no current plans to include additional genomes to the SnpEff tool on the public Main Galaxy instance at http://usegalaxy.org. For the ANNOVAR tool, the supported genome at this time is "hg19". When a .vcf file is assigned to that reference genome (aka "database"), the tool form fills out to display the available annotation to select from. This tool is a brand-new implementation and still undergoing development, so I cannot comment yet about future plans. The best solution is to either run a local Galaxy (with sufficient resources) or what is probably more practical for many scientific end users, a cloud Galaxy or possibly a Slipstream Appliance. The tool wrappers for both tools are in the Tool Shed, so it can be installed and used within your Galaxy, where you can add in any genome that you want that has the appropriate reference data available. The reference data formats can be found on the originating tool sites with supplemental help notes in the Tool Shed repositories. Help to get started is in these links: https://wiki.galaxyproject.org/BigPicture/Choices https://wiki.galaxyproject.org/Tool%20Shed Hopefully one of these solutions will work out you. If there is more to share, we will send a followup reply, Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org

ADD COMMENT • link written 4.8 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen, thanks for your answer! Unfortunatelly I cannot run Galaxy locally (in my Institute we only have Windows computers), but I can try on a cloud. I have a DIAG account, do you know if Galaxy works there? Debora

ADD REPLY • link written 4.8 years ago by garzetti • 100

Hello, is there a tool in the main Galaxy to extract a fasta alignment of my detected variants from a vcf file? I have 19 samples (plus the reference). Thanks! Debora

ADD REPLY • link written 4.8 years ago by garzetti • 100

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