Kevin:

Yes, for Illumina data BWA would be the best option from what is currently 
available at the main site. You can then identify variants with pileup and 
compare across the samples much as it is shown at 
http://usegalaxy.org/heteroplasmy. This should give you a rough idea on what to 
expect. However, piplines for proper (1000genomes-like) varinat calling that 
include realignment and recalibration steps are coming by the end of the Summer.

Thanks!

anton

 
Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org



On Jul 13, 2011, at 1:43 PM, Kevin Pawlik PhD wrote:

> Hi, Anton:
>  
> Diploid, 2x50 PE sequencing, rougly 5x coverage per sample. This is low 
> coverage as a “first pass” - does that make a difference in the workflow 
> strategy? Also, would BWA have been the better alignment option?
>  
> Thank you,
>  
> Kevin
>  
> From: Anton Nekrutenko [mailto:an...@bx.psu.edu] 
> Sent: Wednesday, July 13, 2011 9:07 AM
> To: Kevin Pawlik PhD
> Cc: galaxy-user@lists.bx.psu.edu
> Subject: Re: [galaxy-user] Workflow assistance
>  
> Kevin:
>  
> Is this a diploid or haploid organism?
>  
> anton
> galaxy team
>  
>  
> Anton Nekrutenko
> http://nekrut.bx.psu.edu
> http://usegalaxy.org
>  
>  
>  
> On Jul 12, 2011, at 11:38 PM, Kevin Pawlik PhD wrote:
> 
> 
> After viewing tutorials and reading the information associated with various 
> tools, I ask that you point me toward an appropriate workflow for the 
> following:
>  
> I sequenced (Illumina) 5 genomes of phenotype(+) samples and 1 genome of a 
> phenotype(-) control. I uploaded fastqsanger files to Galaxy and performed 
> Bowtie alignments. I want to find the allelic positions where the (+) genomes 
> differ from the (-) genome.
>  
> Many thanks,
>  
> Kevin
>  
>  
>  
>  
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