Variant annotation in galaxy

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Variant annotation in galaxy

garzetti
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
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Re: Variant annotation in galaxy

Jen Hillman-Jackson
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

On 2/24/14 3:39 AM, garzetti 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
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
>  http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
>  http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>
>  http://galaxyproject.org/search/mailinglists/

--
Jennifer Hillman-Jackson
http://galaxyproject.org

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

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Jennifer Hillman-Jackson
http://galaxyproject.org
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Re: Variant annotation in galaxy

garzetti
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
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

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To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

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Concatenate variants from vcf files

garzetti
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
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

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