The MAF file format is a tab-delimited text file format intended for describing somatic DNA mutations detected in sequencing results, and is distinct from the Multiple Alignment Format file type, which is intended for representing aligned nucleotide sequences. Column headers and ordering may sometimes vary between files of different sources, but the names and orders of columns, as defined in the specification, are the following:
Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status4 Validation_Status4 Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer Tumor_Sample_UUID Matched_Norm_Sample_UUID
Many MAF files, such as those available from the TCGA, also contain additional columns expanding on the variant annotation. These columns can include reference nucleotide transcript IDs for corresponding genes, representative codon or amino acid changes, QC metrics, population statistics, and more.