code: def includes_missingalt(data):
      
      MISSINGALT_VERSION = LooseVersion("4.1.0.0")
      version = LooseVersion(broad.get_gatk_version(config=dd.get_config(data)))
      return version >= MISSINGALT_VERSION
docs: As of GATK 4.1.0.0, variants with missing alts are generated
      (see https://github.com/broadinstitute/gatk/issues/5650)