Mutation Annotation Format

MAF is a tab-delimited text file with aggregated mutation information from VCF files and are generated on a project-level. It is often used to describe somatic mutations. In KGGSeq, six columns are required, their header names are fixed but can be in any order. The six columns are:

• Tumor_Sample_UUID: Aliquot UUID for tumor sample.
• Chromosome: The affected chromosome.
• Start_Position: Lowest numeric position of the reported variant on the genomic reference sequence. Mutation start coordinate.
• Reference_Allele: The plus strand reference allele at this position. Includes the deleted sequence for a deletion or "-" for an insertion.
• Tumor_Allele1: Primary data genotype for tumor sequencing (discovery) allele 1. A "-" symbol for a deletion represents a variant. A "-" symbol for an insertion represents wild-type allele. Novel inserted sequence for insertion does not include flanking reference bases.
• Tumor_Allele2: Tumor sequencing (discovery) allele 2.

There is an example:

Tumor_Sample_UUID    Chromosome    Start_Position    Reference_Allele    Tumor_Allele1    Tumor_Allele2
TCGA-A8-A06P    chr19    58864307    C    A    C
TCGA-A8-A06P    chr19    58864307    C    A    C
TCGA-E9-A1NH    chr19    58864366    G    A    G
TCGA-E9-A22B    chr19    58862784    C    T    C
TCGA-BH-A0HP    chr10    52595854    G    A    G
TCGA-BH-A18P    chr10    52595937    G    A    G
TCGA-A2-A0EY    chr12    9246090    C    T    C
TCGA-A8-A08G    chr12    9251298    G    A    G
TCGA-B6-A0IC    chr12    9220358    -    T    -