![]() Lowest numeric position of the reported variant on the genomic reference sequence. Hg18, hg19, GRCh37, GRCh37-lite, 36, 36.1, 37,Ĭhromosome number without "chr" prefix that contains the gene. Non-GSC centers will be also supported if center name is an accepted center name.Īny TGCA accepted genome identifier. If multiple institutions report the same mutation separate list using semicolons. Genome sequencing center reporting the variant. If no gene exists within 3kb enter "Unknown".Įntrez gene ID (an integer). HUGO symbol for the gene (HUGO symbols are always in all caps). Optional columns are not validated by the DCC and can be in any order. Any columns that come after the columns described in Table 1 are The validator looks for a header stating the version of the Columns may allow null values (i.e._ blank cells) and/or haveĮnumerated values. Column headers and values are case sensitive where In Table 1 and are required in every MAF file. The format of a MAF file is tab-delimited columns. These files are deployed as protected data. These files are deployed as open access data. There is no such constraint for experimentally validated ( Validation_Statusis "Valid") somatic mutations.ĭbSNP sites that are not annotated as somatic in dbSNP, COSMIC or OMIM must be removed from somatic MAFs. SOMATIC = (A AND (B OR C OR D)) OR (E AND F)ĭ. When Mutation_Status is None,Ĭenters need to make sure that Mutations_Status "None" doesn't includeįor a somatic MAF, following rules should be satisfied: "Somatic" and "None" are the only acceptable values for "Mutation_Status"įor a somatic.MAF (named. ![]() The following items in the specification were added or modified in version 2.4.1 ![]() This current revision is version 2.4.1 of the Mutation Annotation Format Specification for Mutation Annotation Format AdditionalĬhanges are the removal of the "under construction" banner, changing all text toīlack, and fixing a typo in the link to the MAF 2.2 specification. The spec has been reverted to the June 26th version (version 20). That was available during the active period of the TCGA project. This definition was taken from the previously public wiki hosted by TCGA and reflects the MAF format Mutation Annotation Format (MAF) - Legacy TCGA Specification fa-file-text Download PDF /Data/PDF/Data_UG.pdf.Bioinformatics Pipeline: Protein Expression.Bioinformatics Pipeline: Methylation Analysis Pipeline.Bioinformatics Pipeline: Copy Number Variation Analysis.Bioinformatics Pipeline: miRNA Analysis.Bioinformatics Pipeline: DNA-Seq Analysis.fa-file-text Download PDF /Data_Transfer_Tool/PDF/Data_Transfer_Tool_UG.pdf.Data Transfer Tool Command Line Documentation.fa-file-text Download PDF /Data_Submission_Portal/PDF/Data_Submission_Portal_UG.pdf.Before Submitting Data to the GDC Portal.fa-file-text Download PDF /Data_Portal/PDF/Data_Portal_UG.pdf.fa-file-text Download PDF /API/PDF/API_UG.pdf.Appendix C: Format of Submission Queries and Responses.
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