Realignment and recalibration is not yet possible on the main site. However, we are working on several re-sequencing projects in house where these tools are used and will bring them to Galaxy by ISMB conference in Vienna.
The indel analysis at the moment is rather simplistic (yet still very useful) and is based on processing on CIGAR strings in aligned SAM files. You can simply run datasets generated by BWA through our indels tools.
Thanks and let us know if you have more questions.
On Apr 8, 2011, at 7:42 AM, Mike Dufault wrote:
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