VCF files are used to report sequence variations (e..g., SNPs, indels and larger structural variants) together with rich annotations. VCF files are modular where the annotations and genotype information for a variant are separated from the call itself. VCF version 4.1 is the currently active format specification.
GSCs generate sequence variation data using high-throughput sequencing technologies and resulting variations can be submitted to the DCC as VCF files. TCGA has adopted VCF 4.1 with certain modifications to support supplemental information specific to the project. The specification describes the format TCGA VCF files should follow and validation steps that have been implemented at the DCC.