Relevant classes: * [MafUtil](https://github.com/cBioPortal/cbioportal/blob/master/core/src/main/java/org/mskcc/cbio/maf/MafUtil.java) * [ExtendedMutationUtil](https://github.com/cBioPortal/cbioportal/blob/master/core/src/main/java/org/mskcc/cbio/portal/util/ExtendedMutationUtil.java) * [MafRecord](https://github.com/cBioPortal/cbioportal/blob/master/core/src/main/java/org/mskcc/cbio/maf/MafRecord.java) ### [MafUtil](https://github.com/cBioPortal/cbioportal/blob/master/core/src/main/java/org/mskcc/cbio/maf/MafUtil.java) - to - cBioPortal Database mapping. | MafUtil Field Names | MAF Column Name | `MUTATION.` | `MUTATION_EVENT.` | NOTES | | -------------------------------- | -------------------------------- | -------------------------------------------------------- | ---------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | HUGO_SYMBOL | Hugo_Symbol | | | Helps resolve CanonicalGene (default by Entrez Gene id) | | ENTREZ_GENE_ID | Entrez_Gene_Id | mutation.entrez_gene_id | mutation_event.entrez_gene_id | References gene.entrez_gene_id | | CENTER | Center | mutation.center | | | | NCBI_BUILD | NCBI_Build | | mutation_event.ncbi_build | | | CHROMOSOME | Chromosome | | mutation_event.chr | | | START_POSITION | Start_Position | | mutation_event.start_position | | | END_POSITION | End_Position | | mutation_event.end_position | | | STRAND | Strand | | mutation_event.strand | | | VARIANT_CLASSIFICATION | Variant_Classification | | mutation_event.mutation_type ** | see ExtendedMutationUtil.getMutationType() | | VARIANT_TYPE | Variant_Type | | mutation_event.variant_type | | | REFERENCE_ALLELE | Reference_Allele | | mutation_event.reference_allele | | | TUMOR_SEQ_ALLELE_1 | Tumor_Seq_Allele1 | mutation.tumor_seq_allele1 | mutation_event.tumor_seq_allele | see MafUtil.resolveTumorSeqAllele() | | TUMOR_SEQ_ALLELE_2 | Tumor_Seq_Allele2 | mutation.tumor_seq_allele2 | mutation_event.tumor_seq_allele | see MafUtil.resolveTumorSeqAllele() | | DBSNP_RS | dbSNP_RS | | mutation_event.db_snp_rs | | | DBSNP_VAL_STATUS | dbSNP_Val_Status | | mutation_event.db_snp_val_status | | | TUMOR_SAMPLE_BARCODE | Tumor_Sample_Barcode | mutation.sample_id | | sample.stable_id / sample.internal_id | | MATCHED_NORM_SAMPLE_BARCODE | Matched_Norm_Sample_Barcode | mutation.matched_norm_sample_barcode | | | | MATCH_NORM_SEQ_ALLELE1 | Match_Norm_Seq_Allele1 | mutation.match_norm_seq_allele1 | | | | MATCH_NORM_SEQ_ALLELE2 | Match_Norm_Seq_Allele2 | mutation.match_norm_seq_allele2 | | | | TUMOR_VALIDATION_ALLELE1 | Tumor_Validation_Allele1 | mutation.tumor_validation_allele1 | | | | TUMOR_VALIDATION_ALLELE2 | Tumor_Validation_Allele2 | mutation.tumor_validation_allele2 | | | | MATCH_NORM_VALIDATION_ALLELE1 | Match_Norm_Validation_Allele1 | mutation.match_norm_validation_allele1 | | | | MATCH_NORM_VALIDATION_ALLELE2 | Match_Norm_Validation_Allele2 | mutation.match_norm_validation_allele2 | | | | VERIFICATION_STATUS | Verification_Status | mutation.verification_status | | | | VALIDATION_STATUS | Validation_Status | mutation.validation_status | | | | MUTATION_STATUS | Mutation_Status | mutation.mutation_status | | | | SEQUENCING_PHASE | Sequencing_Phase | mutation.sequencing_phase | | | | SEQUENCE_SOURCE | Sequence_Source | mutation.sequence_source | | | | VALIDATION_METHOD | Validation_Method | mutation.validation_method | | | | SCORE | Score | mutation.score | | | | BAM_FILE | BAM_File | mutation.bam_file | | | | SEQUENCER | Sequencer | mutation.sequencer | | | | AMINO_ACID_CHANGE | Amino_Acid_Change | mutation.amino_acid_change | mutation_event.protein_change ** | see ExtendedMutationUtil.getProteinChange() | | T_REF_COUNT | t_ref_count | mutation.tumor_ref_count ** | | see ExtendedMutationUtil.getTumorRefCount() | | T_ALT_COUNT | t_alt_count | mutation.tumor_alt_count ** | | see ExtendedMutationUtil.getTumorAltCount() | | N_REF_COUNT | n_ref_count | mutation.normal_ref_count ** | | see ExtendedMutationUtil.getNormalRefCount() | | N_ALT_COUNT | n_alt_count | mutation.normal_alt_count ** | | see ExtendedMutationutil.getNormalAltCount() | | I_T_REF_COUNT | i_t_ref_count | mutation.tumor_ref_count ** | | see ExtendedMutationUtil.getTumorRefCount() | | AD_REF | AD_Ref | mutation.tumor_ref_count ** | | see ExtendedMutationUtil.getTumorRefCount() | | I_T_ALT_COUNT | i_t_alt_count | mutation.tumor_alt_count ** | | see ExtendedMutationUtil.getTumorAltCount() | | AD_ALT | AD_Alt | mutation.tumor_alt_count ** | | see ExtendedMutationUtil.getTumorAltCount() | | NORM_AD_REF | Norm_AD_Ref | mutation.normal_ref_count ** | | see ExtendedMutationUtil.getNormalRefCount() | | NORM_AD_ALT | Norm_AD_Alt | mutation.normal_alt_count ** | | see ExtendedMutationutil.getNormalAltCount() | | T_TOT_COV | TTotCov | mutation.tumor_ref_count / mutation.tumor_alt_count ** | | see ExtendedMutationUtil.getTumorRefCount() / ExtendedMutationUtil.getTumorAltCount() | | T_VAR_COV | TVarCov | mutation.tumor_ref_count / mutation.tumor_alt_count ** | | see ExtendedMutationUtil.getTumorRefCount() / ExtendedMutationUtil.getTumorAltCount() | | N_TOT_COV | NTotCov | mutation.normal_ref_count / mutation.normal_alt_count ** | | see ExtendedMutationUtil.getNormalRefCount() / ExtendedMutationUtil.getNormalAltCount() | | N_VAR_COV | NVarCov | mutation.normal_ref_count / mutation.normal_alt_count ** | | see ExtendedMutationUtil.getNormalRefCount() / ExtendedMutationUtil.getNormalAltCount() | | TUMOR_DEPTH | tumor_depth | mutation.tumor_ref_count / mutation.tumor_alt_count ** | | see ExtendedMutationUtil.getTumorRefCount() / ExtendedMutationUtil.getTumorAltCount() | | TUMOR_VAF | tumor_vaf | mutation.tumor_ref_count / mutation.tumor_alt_count ** | | see ExtendedMutationUtil.getTumorRefCount() / ExtendedMutationUtil.getTumorAltCount() | | NORMAL_DEPTH | normal_depth | mutation.normal_ref_count / mutation.normal_alt_count ** | | see ExtendedMutationUtil.getNormalRefCount() / ExtendedMutationUtil.getNormalAltCount() | | NORMAL_VAF | normal_vaf | mutation.normal_ref_count / mutation.normal_alt_count ** | | see ExtendedMutationUtil.getNormalRefCount() / ExtendedMutationUtil.getNormalAltCount() | | PROTEIN_CHANGE | HGVSp_Short | | mutation_event.protein_change ** | see ExtendedMutationUtil.getProteinChange() | | CODONS | Codons | | mutation_event.oncotator_codon_change ** | see ImportExtendedMutation (codonChange = record.getCodons()) / MAF field "Codons" always overrides MAF value ONCOTATOR_CODON_CHANGE // "ONCOTATOR_CODON_CHANGE" never used? | | SWISSPROT | SWISSPROT | | mutation_event.oncotator_uniprot_accession ** | see ImportExtendedMutation (uniprotAccession = record.getSwissprot()) / if current accession type is SwissProt then record.getSwissprot() = uniprotAccession OR DaoUniProtIdMapping.mapFromUniprotIdToAccession(uniprotName) where uniprotName = record.getSwissprot() / OVERRIDES MAF field "ONCOTATOR_UNIPROT_ACCESSION" | | REFSEQ | RefSeq | | mutation_event.oncotator_refseq_mrna_id ** | see ImportExtendedMutation(refseqMrnaId = record.getRefSeq()) / Always overrides MAF field "ONCOTATOR_REFSEQ_MRNA_ID" | | PROTEIN_POSITION | Protein_position | | mutation_event.oncotator_protein_pos_start / mutation_event.oncotator_protein_pos_end ** | see ExtendedMutationUtil.getProteinPosStart() / resolved from record.getProteinPosition() or record.getProteinChange() based on what is avialable / MAF field "ONCOTATOR_PROTEIN_POS_START" and "ONCOTATOR_PROTEIN_POS_END" never used? | | ONCOTATOR_VARIANT_CLASSIFICATION | ONCOTATOR_VARIANT_CLASSIFICATION | | mutation_event.mutation_type ** | see ExtendedMutationUtil.getMutationType() | | ONCOTATOR_REFSEQ_MRNA_ID | ONCOTATOR_REFSEQ_MRNA_ID | | mutation_event.oncotator_refseq_mrna_id ** [maps to DB but MAF value never imported] | see ImportExtendedMutation(refseqMrnaId = record.getRefSeq()) / Always overrides MAF field "ONCOTATOR_REFSEQ_MRNA_ID" / MafRecord (record.getOncotatorRefseqMrnaId()) never used | | ONCOTATOR_UNIPROT_ENTRY_NAME | ONCOTATOR_UNIPROT_ENTRY_NAME | | mutation_event.oncotator_uniprot_entry_name ** [maps to DB but MAF value never imported] | see ImportExtendedMutation (record.getOncotatorUniprotName() never used to set mutation_event.oncotator_uniprot_entry_name) / MafRecord (record.getOncotatorUniprotName()) never used | | ONCOTATOR_UNIPROT_ACCESSION | ONCOTATOR_UNIPROT_ACCESSION | | mutation_event.oncotator_uniprot_accession ** [maps to DB but MAF value never imported] | see ImportExtendedMutation (uniprotAccession = record.getSwissprot()) / if current accession type is SwissProt then record.getSwissprot() = uniprotAccession OR DaoUniProtIdMapping.mapFromUniprotIdToAccession(uniprotName) where uniprotName = record.getSwissprot() / OVERRIDES MAF field "ONCOTATOR_UNIPROT_ACCESSION" / MafRecord (record.getOncotatorUniprotAccession()) never used | | ONCOTATOR_CODON_CHANGE | ONCOTATOR_CODON_CHANGE | | mutation_event.oncotator_codon_change ** [maps to DB but MAF value never imported] | see ImportExtendedMutation (codonChange = record.getCodons()) / MAF field "Codons" always overrides MAF value ONCOTATOR_CODON_CHANGE // "ONCOTATOR_CODON_CHANGE" never used? / MafRecord (record.getOncotatorCodonChange()) never used | | ONCOTATOR_PROTEIN_POS_START | ONCOTATOR_PROTEIN_POS_START | | mutation_event.oncotator_protein_pos_start ** [maps to DB but MAF value never imported] | see ExtendedMutationUtil.getProteinPosStart() / resolved from record.getProteinPosition() or record.getProteinChange() based on what is avialable / MAF field "ONCOTATOR_PROTEIN_POS_START" never used? | | ONCOTATOR_PROTEIN_POS_END | ONCOTATOR_PROTEIN_POS_END | | mutation_event.oncotator_protein_pos_end ** [maps to DB but MAF value never imported] | see ExtendedMutationUtil.getProteinPosStart() / resolved from record.getProteinPosition() or record.getProteinChange() based on what is avialable / MAF field "ONCOTATOR_PROTEIN_POS_END" never used? | | DRIVER_FILTER | cbp_driver | mutation.driver_filter | | | | DRIVER_FILTER_ANNOTATION | cbp_driver_annotation | mutation.driver_filter_annotation | | | | DRIVER_TIERS_FILTER | cbp_driver_tiers | mutation.driver_tiers_filter | | | | DRIVER_TIERS_FILTER_ANNOTATION | cbp_driver_tiers_annotation | mutation.driver_tiers_filter_annotation | | |