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Old 07-24-2014, 06:03 AM   #2
Rick Westerman
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104

bedtools always comes to mind when asking questions like "how to extract sequence". It should be easy to convert the VCF single coordinate into the start & end coordinates for a BED file (Excel or other spreadsheet program or a simple Perl/Python script). Then use fastaFromBed.
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