Thanks for this. Yes, we are looking at this and the plan is to make SAM the default output for mappers and to initially utilize SAMTools for SNP and indel calling. This will work nicely with Galaxy's BWA and Bowtie wreppers we are working on.



On Jul 24, 2009, at 1:19 PM, Dave Clements wrote:

Hello all,

I just scanned the recent thread started by Abhi Pratap, titled "Experience with Loading NGS data on standalone instance of galaxy"

I didn't see any mention of the SAMtools in that thread.  SAMtools is a platform neutral set of formats and programs for next generations sequence data.  See http://samtools.sourceforge.net/ for more.

Has the Galaxy team considered adding support for SAMtools formats?  It might be a way to deal with all the NGS platforms with a single set of code. 

Dave C.

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