Thanks Erik,

I was also not very clear about Freebayes use in CNV detection. Thanks for clarifiaction.

Mathew

From: Erik Garrison <erik.garrison@bc.edu>
To: Mathew Bunj <mathewbunj@yahoo.com>
Cc: shamsher jagat <kanwarjag@gmail.com>; Jennifer Jackson <jen@bx.psu.edu>; "galaxy-user@lists.bx.psu.edu" <galaxy-user@lists.bx.psu.edu>
Sent: Thursday, August 16, 2012 3:12 PM
Subject: Re: [galaxy-user] copy number variation detcetion in Glaxay

Hi Mathew,

To clarify, freebayes is not designed to detect CNVs. It can CNV information detected in another method to correctly genotype at sites with copy number variations.

If you have exome data, there is conifer http://conifer.sourceforge.net/conifer.sourceforge.net /.

For more general applications, there is ERDS, http://www.duke.edu/~mz34/erds.htm

I don't know if either of these will suit your needs. I use the CNV input methods in freebayes regularly for known, large variations in copy number, such as are seen on mammalian sex chromosomes.

Best,
Erik

On Aug 16, 2012 11:11 AM, "Mathew Bunj" <mathewbunj@yahoo.com> wrote:

Thanks Jen,

I am also intrested in this. Has any one used FreeBayes in Galaxy or out side Gaaxy to detect CNV from a ilumina sequencing data. Is their a tutorial for running this tools.

Thanks.

From: Jennifer Jackson <jen@bx.psu.edu>
To: shamsher jagat <kanwarjag@gmail.com>
Cc: galaxy-user@lists.bx.psu.edu
Sent: Thursday, August 16, 2012 12:48 AM
Subject: Re: [galaxy-user] copy number variation detcetion in Glaxay

Hello,

The tool "FreeBayes" may be of interest. Please see the tool form for
links to the primary tool documentation to see if the functionality will
meet your needs.

Best,

Jen
Galaxy team

On 8/15/12 4:46 AM, shamsher jagat wrote:
> Is there any tool/ combination of tools with in galaxy which can detect
> CNV. I have 100X paired sequencing data between cancer and normal.
> Thanks
>
>
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--
Jennifer 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
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use the Galaxy Development list:

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please use the interface at:

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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/