Here’s a simple exome analysis pipeline using VarScan for variant calling and 
ANNOVAR for annotation:

https://usegalaxy.org/u/jeremy/w/exome-analysis

You may want to tweak some aspects of it, such as using FreeBayes rather than 
VarScan and/or using a different set of annotations from ANNOVAR.

Best,
J.

--
Jeremy Goecks
Assistant Professor, Computational Biology Institute
George Washington University



On Mar 14, 2014, at 9:01 PM, Björn Grüning <bjoern.gruen...@gmail.com> wrote:

> Hi,
> 
> we are currently working on one pipeline. I can share if you are interested, 
> but its not yet finished, parameter wise, but all tools should be there.
> 
> We tried to stick to the GATK2 best-practise guide and are using snpeff for 
> annotation.
> 
> Cheers,
> Bjoern
> 
> Am 15.03.2014 01:55, schrieb Mathew Bunj:
>> No I have not received any feedback as yet.
>> 
>> Thanks
>> 
>> 
>> 
>> On Friday, March 14, 2014 7:42 AM, Kristin Kernohan 
>> <kristinkerno...@gmail.com> wrote:
>> 
>> Hi
>> 
>> did anyone answer this? Id be curious to know as well
>> 
>> thanks
>> 
>> Kristin
>> 
>> 
>> 
>> On Thu, Mar 13, 2014 at 10:22 PM, Mathew Bunj <mathewb...@yahoo.com> wrote:
>> 
>> I was wondering if Galaxy has any work flow for calling mutations in Exome 
>> seq and then annotating. Alignment can be done by BWA.
>>> 
>>> 
>>> Thanks
>>> 
>>> 
>>> Mathew
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___________________________________________________________
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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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