bioinformatics Common File Formats Mutation Annotation Format (MAF)


Example

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.