def printPairedDellyTransApp(FH, tabCount, mergedTumorBam,
    mergedTumorBamIndex, mergedNormalBam, mergedNormalBamIndex):
    """ Still need to determine how translocations are handled

    Have to run TRA on the bam in its entirety """
    tabs = tabCount * '\t'
    Str = tabs + '### Delly\n' + tabs + """# dellyAnalysisTypes does not need to be defined in this loop
""" + tabs + 'string traAnalysis = "TRA";\n' + tabs + """file dellyTransVcf <single_file_mapper; file=strcat(outDir,"/",patient.patient,".",traAnalysis,".delly.vcf")>;
""" + tabs + """file dellyTransVcfLog <single_file_mapper; file=strcat(outDir,"/",patient.patient,".",traAnalysis,".delly.log")>;
""" + tabs + '(dellyTransVcfLog,dellyTransVcf) = DellyPaired (' + mergedTumorBam + ',' + mergedTumorBamIndex + ',' + mergedNormalBam + ',' + mergedNormalBamIndex + """,patient.patient,outDir,traAnalysis);

""" + tabs + '# Add translocation vcf to contig vcfs\n' + tabs + """DellyPairedContigVcfs << dellyTransVcf;

"""
    FH.write(Str)
    return
