using SnpEff and SNPSift in Galaxy

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using SnpEff and SNPSift in Galaxy

shamsher jagat
I have a VCF file and I want to filter it for nonsynonymous/ deletion/ insertion  seq variations. Once I filter this file and compare between tumor vs normal samples and then annotate such variations.  I believe I can filter this file using SnpSift and then can annotate with SnpEff, When I try to use Snsift filter it just says arbitrary expression. Are there rules how to use expression for a particular filter with in galaxy. If  any one has used SnpSift in galaxy may share their expertise.

Thanks
Kanwar

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Re: using SnpEff and SNPSift in Galaxy

Jen Hillman-Jackson
Hi Kanwar,

This tool in Galaxy uses the same expressions as the line command version (to my knowledge). A list of the possible expressions is listed here. The parenthesis are optional when there is just a single expression.
http://snpeff.sourceforge.net/SnpSift.html#filter

Hopefully this helps,

Jen
Galaxy team

On 12/30/13 2:58 PM, shamsher jagat wrote:
I have a VCF file and I want to filter it for nonsynonymous/ deletion/ insertion  seq variations. Once I filter this file and compare between tumor vs normal samples and then annotate such variations.  I believe I can filter this file using SnpSift and then can annotate with SnpEff, When I try to use Snsift filter it just says arbitrary expression. Are there rules how to use expression for a particular filter with in galaxy. If  any one has used SnpSift in galaxy may share their expertise.

Thanks
Kanwar


___________________________________________________________
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:

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