code: public static final boolean isSameVariantSite(Variant.Builder variant1, Variant variant2) {
      return variant1.getReferenceName().equals(variant2.getReferenceName())
          && variant1.getReferenceBases().equals(variant2.getReferenceBases())
          && variant1.getStart() == variant2.getStart();
    }
docs: Determine whether two variants occur at the same site in the genome, where "site"
  is defined by reference name, start position, and reference bases.
  
  The reference bases are taken into account particularly for indels.
  
  @param variant1
  @param variant2
  @return true, if they occur at the same site