Exome seq work flow

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Exome seq work flow

Mathew Bunj
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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Re: Exome seq work flow

Mathew Bunj
No I have not received any feedback as yet.

Thanks


On Friday, March 14, 2014 7:42 AM, Kristin Kernohan <[hidden email]> 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 <[hidden email]> 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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Re: Exome seq work flow

Björn Grüning-2
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 <[hidden email]> 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 <[hidden email]> 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
>> ___________________________________________________________
>> 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/
>>
>> To search Galaxy mailing lists use the unified search at:
>>
>>    http://galaxyproject.org/search/mailinglists/
>>
>>
>>
>> ___________________________________________________________
>> 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/
>>
>> To search Galaxy mailing lists use the unified search at:
>>
>>    http://galaxyproject.org/search/mailinglists/
___________________________________________________________
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Re: Exome seq work flow

Jeremy Goecks-3
Here’s a simple exome analysis pipeline using VarScan for variant calling and ANNOVAR for annotation:


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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
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please use the interface at:

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To search Galaxy mailing lists use the unified search 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:

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To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

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To search Galaxy mailing lists use the unified search at:

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___________________________________________________________
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To search Galaxy mailing lists use the unified search at:

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___________________________________________________________
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