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Question: Galaxy, Ngs Data, And Samtools?
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gravatar for Dave Clements
9.4 years ago by
Dave Clements • 10
Dave Clements • 10 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. -- Register now for the August GMOD Meeting: http://gmod.org/wiki/August_2009_GMOD_Meeting
gmod samtools bam • 821 views
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modified 9.4 years ago by Anton Nekrutenko ♦ 1.7k • written 9.4 years ago by Dave Clements • 10
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gravatar for Anton Nekrutenko
9.4 years ago by
Anton Nekrutenko ♦ 1.7k
Penn State
Anton Nekrutenko ♦ 1.7k wrote:
Dave: 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. Thanks, a. Anton Nekrutenko http://nekrut.bx.psu.edu http://galaxyproject.org
ADD COMMENT • link written 9.4 years ago by Anton Nekrutenko ♦ 1.7k
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