I have an mpileup tool for Galaxy I've developed.  After a little more testing 
I may be able to share it.

the tool also converts the bcl output of mpileup to vcf


On Oct 12, 2011, at 2:41 PM, Jennifer Jackson wrote:

> Hello David,
> 
> An update is planned, but we can't provide an exact time-line yet. To track 
> the issue, this bitbucket ticket can be followed:
> https://bitbucket.org/galaxy/galaxy-central/issue/524/
> 
> Apologies for the delay in reply,
> 
> Best,
> 
> Jen
> Galaxy team
> 
> On 8/23/11 9:10 AM, David Hoover wrote:
>> Is there any good reason why Galaxy can't use a more recent version of 
>> samtools?  The only difference I can see is the mpileup command.  The 
>> algorithm by which mpileup finds SNPs is a little different.  Does anyone 
>> know if the file format has changed?  The only files that need to change are 
>> sam_pileup.py and sam_pileup.xml.
>> 
>> David Hoover
>> Helix Systems Staff
>> http://helix.nih.gov
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> -- 
> Jennifer Jackson
> http://usegalaxy.org
> http://galaxyproject.org/Support
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--
Glen L. Beane
Senior Software Engineer
The Jackson Laboratory
(207) 288-6153


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