code: def run(_, data, out_dir):
      
      out = []
      vcinfo = get_active_vcinfo(data)
      if vcinfo:
          if dd.get_phenotype(data) == "normal" and "germline" in vcinfo:
              out.append(_bcftools_stats(data, out_dir, "germline", germline=True))
          elif dd.get_phenotype(data) != "germline":
              out.append(_bcftools_stats(data, out_dir))
              if "germline" in vcinfo:
                  out.append(_bcftools_stats(data, out_dir, "germline", germline=True))
          else:
              out.append(_bcftools_stats(data, out_dir, germline=True))
      out.append(_snpeff_stats(data, out_dir))
  
      out = [item for item in out if item]
      if out:
          return {"base": out[0], "secondary": out[1:]}
docs: Prepare variants QC analysis: bcftools stats and snpEff output.