Variant Call Format

The Variant Call Format (VCF) specifies the format of a text file used in bioinformatics for storing gene sequence variations. The format has been developed with the advent of large-scale genotyping and DNA sequencing projects, such as the 1000 Genomes Project. Existing formats for genetic data such as General feature format (GFF) stored all of the genetic data, much of which is redundant because it will be shared across the genomes. By using the variant call format only the variations need to be stored along with a reference genome. The Variant Call Format (VCF) specifies the format of a text file used in bioinformatics for storing gene sequence variations. The format has been developed with the advent of large-scale genotyping and DNA sequencing projects, such as the 1000 Genomes Project. Existing formats for genetic data such as General feature format (GFF) stored all of the genetic data, much of which is redundant because it will be shared across the genomes. By using the variant call format only the variations need to be stored along with a reference genome. The standard is currently in version 4.3, although the 1000 Genomes Project has developed its own specification for structural variations such as duplications, which are not easily accommodated into the existing schema. There is also a Genomic VCF (gVCF) extended format, which includes additional information about 'blocks' that match the reference and their qualities. A set of tools is also available for editing and manipulating the files. The header begins the file and provides metadata describing the body of the file. Header lines are denoted as starting with .mw-parser-output .monospaced{font-family:monospace,monospace}#. Special keywords in the header are denoted with ##. Recommended keywords include fileformat, fileDate and reference.