Does REF of a SNP in vcf must same as referance genome?
Does REF in VCF refer to the base of the reference genome or the base that is the majority of the population? My purpose is to add some VCF made by others into my VCF. My population is mainly INDICA, and his mainly JAPONICA, though we all compare them to the JAP reference genome, will the REF of a site would be different due to different populations? IE, ref-genome is A, my vcf is T, and his was G. After all I havn't seen any locus that MAF=0.95.
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no. https://en.wikipedia.org/wiki/Reference_genome#Human_reference_genome