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Old 11-29-2011, 02:21 PM   #3
swbarnes2
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Location: San Diego

Join Date: May 2008
Posts: 912
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So you want the union of both files? Try vcftools or BEDTools.

I don't think that mpileup will work with vcf files. What it will allow you to do is to take multiple .bams at once, and make one multi-vcf. But if you don't have the .bams, that won't help much.
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