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://<http://conifer.sourceforge.net/> conifer.sourceforge.net/ <http://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" <mathewb...@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 <j...@bx.psu.edu> > *To:* shamsher jagat <kanwar...@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 > > > > > > ___________________________________________________________ > > 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/ > > > > -- > 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 > 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/ > > > > ___________________________________________________________ > 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/ >
___________________________________________________________ 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/
