i have a doubt. i have been analyzing a vcf file and i wanted to check for some of the SNPs if there was correspondence between REF nucleotide in the vcf and the effective nucleotide in the genome from which the SNP was called. In all cases the nucleotide in the specific location i checked was corresponding to the ALT nucleotide in the vcf. Maybe it's a noobie question, but id be very curious to know why (i was expecting a correspondence to REF nucleotide).
Thanks in advance