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Old 05-23-2013, 03:48 PM   #1
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Default Extract allele frequencies from a VCF file

Is there a tool to extract allele frequencies from a VCF file? I looked into vcftools, but that does not seem to be one of the options.

I currently parse out the frequencies manually, but every variant caller writes that info slightly differently (for example, sometimes it's AD and other times is DP4). It would be nice if something generic existed.
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