The main consideration is to make sure that the reference resource matches the genomic build of your VCF. i.e. make sure you are using GRCh37 resources for a GRCh37 aligned VCF, or GRCh38 resources for a GRCh38 aligned VCF. dbSNP A vcf from dbSNP can …

example.vcf.gz is a VCF file of three human subjects aligned to GRCh37 and varaint called following the GATK best practices that had been annotated with rsIDs from dbSNP v151 and further annotated using dbNSFP4.0a and snpEff so includes annotations …