Re: [galaxy-user] Exome seq work flow

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.

Re: [galaxy-user] Exome seq work flow

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 Mat

Re: [galaxy-user] Exome seq work flow

No I have not received any feedback as yet. Thanks On Friday, March 14, 2014 7:42 AM, Kristin Kernohan 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 wrote: I was wondering if Galaxy has any work flow for