Begin AnnotateMutation /Namespace=NgsLib ;
Project NameOfProject;
Data NameOfData;
ID IDColumnForMutations;
Chromosome ChromosomeColumn;
Position PositionColumn;
Mutation MutationColumn;
Other OtherColumn1,OtherColumn2,OtherColumn3;
Custom OS_FunctionalMutation20131003,OS_CosmicMutation_V70,OS_Dbsnp138.Full;
Options /ReferenceLibraryID=Human.B37.3 /GeneModelID=UcscCanonicalGene20131119 /GenerateClusteringFlag=False 
/ClusteringFlagWindowSize=100 /GenerateTableland=True  /AnnotateLongestTranscriptOnly=True
/ExportTextFile=False /Output="";
End;

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