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Old 08-18-2012, 11:50 AM   #7
Senior Member
Location: St. Louis

Join Date: Dec 2010
Posts: 535

The annovar input file only needs 5 columns; you can check the website to see the proper format (it's chr/base/base/ref/var for SNPs, check for indels and make sure it makes sense to you). Once you figure that out it should be easy to take your variant files and add 5 initial columns with the correct information; the rest will carry through so you won't lose anything.
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