code: def create_vcf(isomirs, matures, gtf, vcf_file=None):
      
      global STDOUT
      isomirs['sv'] = [_get_reference_position(m) for m in isomirs["isomir"]]
      mirna = isomirs.groupby(['chrom']).sum()
      sv = isomirs.groupby(['chrom', 'mature', 'sv'], as_index=False).sum()
      sv["diff"] = isomirs.groupby(['chrom', 'mature', 'sv'], as_index=False).size().reset_index().loc[:,0]
      pass_pos = _get_pct(sv, mirna)
      if vcf_file:
          with open(vcf_file, 'w') as out_handle:
              STDOUT = out_handle
              pass_pos = liftover(pass_pos, matures)
  
      if gtf:
          vcf_genome_file = vcf_file.replace(".vcf", "_genome.vcf")
          with open(vcf_genome_file, 'w') as out_handle:
              STDOUT = out_handle
              pass_pos = liftover_to_genome(pass_pos, gtf)
docs: Create vcf file of changes for all samples.
      PASS will be ones with > 3 isomiRs supporting the position
           and > 30% of reads, otherwise LOW