code: def gatk_remove_missingalt(in_file, data):
      
      base = in_file.split('.vcf.gz')[0]
      out_file = "%s-nomissingalt%s" % (base, '.vcf.gz')
      if utils.file_exists(out_file):
          return out_file
      no_gzip_out = out_file.replace(".vcf.gz", ".vcf")
      with file_transaction(no_gzip_out) as tx_out_file:
          with utils.open_gzipsafe(in_file) as in_handle, open(tx_out_file, "w") as out_handle:
              for line in in_handle:
                  line = remove_missingalt(line)
                  if line:
                      out_handle.write(line)
      return vcfutils.bgzip_and_index(no_gzip_out, data["config"])
docs: GATK 4.1.0.0 outputs variants that have missing ALTs, which breaks downstream
      tools, this filters those out.