Question: Galaxy, Ngs Data, And Samtools?
gravatar for Dave Clements
9.4 years ago by
Dave Clements10 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 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:
gmod samtools bam • 821 views
ADD COMMENTlink modified 9.4 years ago by Anton Nekrutenko1.7k • written 9.4 years ago by Dave Clements10
gravatar for Anton Nekrutenko
9.4 years ago by
Penn State
Anton Nekrutenko1.7k 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
ADD COMMENTlink written 9.4 years ago by Anton Nekrutenko1.7k
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