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.

Anton Nekrutenko

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:anton@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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