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This article introduces you how to understand Mutation Annotation Format format, the content is very detailed, interested friends can use for reference, I hope it can be helpful to you.

Mutation Annotation Format, referred to as MAF, is a file format developed by TCGA to store mutation annotation information. In TCGA, there are four types of abrupt data

Annotated Somatic Mutation, somatic mutation annotation file in VCF format, annotated by VEP software, the file suffix is vep.vcf.gz

Raw Simple Somatic Mutation, the original file of somatic mutation, format is VCF, file suffix is vcf.gz

The mutation annotation file of Aggregated Somatic Mutation and protected, which requires account number and permission to download. The format is MAF, and the file suffix is maf.gz.

Masked Somatic Mutation, open access mutation comment file, free download, format is MAF, file suffix is maf.gz

In TCGA, VCF is usually used to record the somatic mutation-related results of a single sample, and MAF is used to integrate the somatic mutation annotation results of all samples, so the MAF format is called project-level. According to the openness of the data, it is divided into protected and open access, where open access is the MAF file that we can download directly. Take breast cancer as an example, four MAF files are provided in TCGA.

Corresponding to 4 different somatic mutation calling software, each file contains the somatic SNV annotation results of 1044 samples.

MAF, similar to VCF, is also a plain text format, made up of\ t-separated columns. The screenshot of the MAF file downloaded from GDC is as follows

# begins with a comment line, and the rest is the body. Each column has a fixed header. The complete MAF has more than 100 columns. In actual processing, we may not have so many columns of information. Several commonly used columns are explained as follows.

Column1, Hugo_Symbol, gene symbol provided by HUGO, indicates the name of the gene in which SNV is located

The entrez id of the gene in which the SNV is located. If there is no corresponding gene, it will be represented by 0.

Column 4 reference genome version used in NCBI reference build, snv calling

Column5,Chromsome, the chromosome where SNV is located

The starting position of column6,Start_Position and SNV on chromosomes

The termination position of column7,End_Position,SNV on chromosomes

The classification of column9,Variant_Classification, SNV loci and Missense_Mutation,Nonsense_Mutation is based on the effect of SNV on translation.

Types of column10,Variant_Type and SNV loci, such as SNP, INS,DEl, etc.

Column11,Reference_Allel, allel on the reference genome

Column12,Tumor_Seq_Allel1, the major allele corresponding to this locus in tumor samples

Column13,Tumor_Seq_Allel2, the suballele corresponding to this locus in the tumor sample

Column16,Tumor_Sample_Barcode, barcode of tumor sample

Column17,Tumor_Normal_Barcode, the barcode of the matched normal sample

For the detailed meaning of each column, see the link below

Https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/

MAF is a file format defined specifically for human, which can contain the SNV of all samples and the corresponding annotation information through a single file, which is very convenient for downstream analysis. In practice, VCF files can be converted to MAF format through vcf2maf, and the usage of the software will be described in detail in subsequent articles.

On how to understand the Mutation Annotation Format format to share here, I hope that the above content can be of some help to you, can learn more knowledge. If you think the article is good, you can share it for more people to see.

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