code: def _format_variant(self, case_id, gemini_variant, individual_objs,
                          index=0, add_all_info=False):
          chrom = gemini_variant['chrom']
          if chrom.startswith('chr') or chrom.startswith('CHR'):
              chrom = chrom[3:]
          variant_dict = {
              'CHROM':chrom,
              'POS':str(gemini_variant['start']),
              'ID':gemini_variant['rs_ids'],
              'REF':gemini_variant['ref'],
              'ALT':gemini_variant['alt'],
              'QUAL':gemini_variant['qual'],
              'FILTER':gemini_variant['filter']
          }
          variant = Variant(**variant_dict)
          variant.update_variant_id(gemini_variant['variant_id'])
          logger.debug("Creating a variant object of variant {0}".format(
              variant.variant_id))
          variant['index'] = index
          self._add_most_severe_consequence(variant, gemini_variant)
          self._add_impact_severity(variant, gemini_variant)
          variant.start = int(gemini_variant['start'])
          variant.stop = int(gemini_variant['end'])
          if self.variant_type == 'sv':
              variant.sv_type = gemini_variant['sub_type']
              variant.stop = int(gemini_variant['end'])
              self._add_sv_coordinates(variant)
          else:
              self._add_transcripts(variant, gemini_variant)
              self._add_thousand_g(variant, gemini_variant)
              self._add_exac(variant, gemini_variant)
              self._add_gmaf(variant, gemini_variant)
              if gemini_variant['cadd_scaled']:
                  variant.cadd_score = gemini_variant['cadd_scaled']
              polyphen = gemini_variant['polyphen_pred']
              if polyphen:
                  variant.add_severity('Polyphen', polyphen)
              sift = gemini_variant['sift_pred']
              if sift:
                  variant.add_severity('SIFT', sift)
          self._add_hgnc_symbols(variant)
          if self.variant_type == 'snv':
              self._add_genes(variant)
          self._add_consequences(variant)
          if add_all_info:
              self._add_genotypes(variant, gemini_variant, case_id, individual_objs)
              if self.variant_type == 'sv':
                  self._add_genes(variant)
          return variant