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Question: Exome Seq Work Flow
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gravatar for Mathew Bunj
4.7 years ago by
Mathew Bunj • 100
Mathew Bunj • 100 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 
bwa alignment • 2.1k views
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modified 4.7 years ago • written 4.7 years ago by Mathew Bunj • 100
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gravatar for Mathew Bunj
4.7 years ago by
Mathew Bunj • 100
Mathew Bunj • 100 wrote:
No I have not received any feedback as yet. Thanks Hi did anyone answer this? Id be curious to know as well thanks Kristin I was wondering if Galaxy has any work flow for calling mutations in Exome seq and then annotating. Alignment can be done by BWA.
ADD COMMENT • link written 4.7 years ago by Mathew Bunj • 100
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:
ADD REPLY • link written 4.7 years ago by Bjoern Gruening ♦ 5.1k
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
ADD REPLY • link written 4.7 years ago by Jeremy Goecks ♦ 50
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