i've been using a tool called annovar for this. it is a perl script, but on a
mac or linux box very easy to implement (via terminal window on mac). will
filter based on dnSNP, 1000 genomes or complete genomics datasets. very
straightforward with really no programming ability needed.
rich
________________________________
From: Jennifer Jackson <j...@bx.psu.edu>
To: galaxy-user <galaxy-user@lists.bx.psu.edu>; svem...@uthsc.edu
Sent: Tuesday, October 4, 2011 9:24 PM
Subject: [galaxy-user] 1000 genome variant calls
Repost
-------- Original Message, Please send all replies to "all" --------
Hello Jennifer,
I am a new to Linux and have no programming skills and hence galaxy is the only
rescuer for me.
I have nextgen dna seq data. I finished analysis and now have a list of
variants. I want to see if these variants are already in 1000 genome data
released in Aug 2011. I want to upload list of my chromosome locations and see
if they are any matches with 1000 genome data.
IS there a way we can do it in galaxy...instead of writing scripts to do it.
Like I said, I have no programming skills.
Thanks.
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___________________________________________________________
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/