A VCF file is generated through variant calling which basically uses alignment to identify the variants. If I have an unknown VCF and I know which reference genome was used to generate it, can I map the variations to the reference genome without going through the alignment process?
Abhijeet Singh
i dont think if it is possible or preferred. Alignment only could really give the information about the variation.
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Emily Perry
I'm not sure I understand your question. You've got a VCF and the reference genome it goes with. Are you looking to generate the sequence of the variant genome? If so, there's a BioStars question that covers this and gives a few options: https://www.biostars.org/p/121643/
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