File formats


Mutations are provided in a Mutation Annotation Format (MAF) file (specification here). Columns can be in any order, and only a few columns in the MAF file are needed. The following is a list of the required columns.

  • Hugo_Symbol

  • Chromosome

  • Start_Position

  • End_Position

  • Reference_Allele

  • Tumor_Seq_Allele2

  • Tumor_Sample_Barcode

  • Variant_Classification

The remaining columns in the MAF specification can be left empty or not included.

Only coding variants found in the Variant_Classification column will be used, which includes the following: ‘Missense_Mutation’, ‘Silent’, ‘Nonsense_Mutation’, ‘Splice_Site’, ‘Nonstop_Mutation’, ‘Translation_Start_Site’, ‘Frame_Shift_Ins’, ‘Frame_Shift_Del’, ‘In_Frame_Ins’, or ‘In_Frame_Del’.