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Old 10-01-2012, 06:16 AM   #2
ekg
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Location: Boston, MA

Join Date: Apr 2010
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For comparing case and control VCFs you can generate a kind of overlap comparison using this script and the utilities in vcflib: https://github.com/ekg/vcflib/blob/master/vcfmultiway.

For generating the variant calls, you have a lot of options
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