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 <jen@bx.psu.edu>
To: galaxy-user <galaxy-user@lists.bx.psu.edu>; svemula@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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