I have a raw vcf from cgatools build long time ago, from the header I can tell it is build using
##source_GENE_ANNOTATIONS=NCBI build 37.1
I used annovar to annotate it using hg19, I feel many positions has 'dot' in the annotation. I am afraid I am annotating to the wrong reference.
The raw vcf we have longtime ago (build37) , is annotating it with hg19 wrong? Again appology for naive questions, still hunting the filed :)