VCF location in consensus sequence

nupurgupta

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VCF location in consensus sequence

07-20-2012, 01:47 PM

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
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