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  • #1

    VCF location in consensus sequence

    Hi,
    I have a VCF file created by running GATK on read files against a reference genome. The variants in the VCF file have 'locations', these are the locations on the reference genome. I also have a consensus sequence created by vcftools. What I need thought is the variant location on the consensus sequence. (And then I will need to get annotation data for that region.)
    Any idea how this can be done please- getting variant consensus locations?
    Much appreciated
    Last edited by nupurgupta; 07-20-2012, 01:47 PM. Reason: tags
    Tags: None
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