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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