1000 Genome Variant Calls

Question: 1000 Genome Variant Calls

7.2 years ago by

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Repost 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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modified 7.2 years ago by Richard Mark White • 240 • written 7.2 years ago by Jennifer Hillman Jackson ♦ 25k

7.2 years ago by

Richard Mark White • 240

Richard Mark White • 240 wrote:

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 ________________________________ To: galaxy-user <galaxy-user@lists.bx.psu.edu>; svemula@uthsc.edu Subject: [galaxy-user] 1000 genome variant calls Repost 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. ___________________________________________________________ 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/

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