No I have not received any feedback as yet. Thanks On Friday, March 14, 2014 7:42 AM, Kristin Kernohan <kristinkernohan@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 <mathewbunj@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 ___________________________________________________________ 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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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 <kristinkernohan@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 <mathewbunj@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 ___________________________________________________________ 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:
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:
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To manage your subscriptions to this and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at:
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.gruening@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 <kristinkernohan@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 <mathewbunj@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 ___________________________________________________________ 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:
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:
To search Galaxy mailing lists use the unified search at:
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:
To search Galaxy mailing lists use the unified search at:
participants (3)
-
Björn Grüning -
Jeremy Goecks -
Mathew Bunj