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:
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/
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.
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