Imported MAF Columns
Relevant classes:
MafUtil - to - cBioPortal Database mapping.
| MafUtil Field Names | MAF Column Name | MUTATION.<FIELD> |
MUTATION_EVENT.<FIELD> |
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 |