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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