I have SNP data from an array which has coordinate information from an older version of the genome (in VCF form). I want to annotate it using GTF/GFF file of the current version of the genome using SnpEff or ANNOVAR or VEP. Do I need to take care of the VCF coordinates somehow (like liftover) so that the variant annotation program can annotate the variants correctly?
Or, the variant annotation program will only annotate the variants with matching coordinates and incorrectly annotate the rest whose coordinates don't match?
I am assuimg its the second, but want other people's opinion on this.