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Old 12-05-2011, 10:14 AM   #2
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Location: Research Triangle Park, NC

Join Date: Aug 2009
Posts: 245

PacBio's SMRT suite has a python script to supposedly go from GFFv4 to VCF.

But, I recall on the BEDTools discussion board, Aaron Quinlan has mentioned that going from GFF or BED to VCF is not a simple task, unless the input files were originally created to track all the information required for the VCF output. That makes it difficult to write generic scripts for conversion.
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