Variant Call Format

The Variant Call Format Specification VCFv4.3 and BCFv2.2 (Superseded by the VCF v4.4 and v4.5 specifications) 5 Nov 2025 The master version of this document can be found at This printing is version c101c79 from that repository, last modified on the date shown above. 1 tively), ∗ Flag, Character, and String. For the Integer type, the values from −2 31 to −2 31 7 cannot be stored in the binary version and therefore are disallowed in both VCF and BCF, see 6.3.3. 1.4 Meta-information lines File meta-information lines start with “ ” and must appear first in the VCF file, before the header line (section 1.5) and data record lines (section 1.6). They may be either unstructured or structured. An unstructured meta-information line consists of a key (denoting the type of meta-information recorded) and a value (which may not be empty and must not start with a ‘<’ character), separated by an ‘=’ character: key=value Several unstructured meta-information lines are defined in this specification, notably fileformat. Others not defined by this specification, e.g. fileDate and source, are commonly found in VCF files. These typically have meanings that are obvious, or they are immaterial for processing the file, or both. A structured meta-information line is similar, but the value is itself a comma-separated list of key=value pairs, enclosed within ‘<’ and ‘>’ characters: key=<key=value,key=value,key=value,. . . > All structured lines require an ID which must be unique within their type, i.e., within all the meta-information lines with the same “ key=” prefix. For all of the structured lines ( INFO, FORMAT, FILTER, etc.) described in this specification, extra fields can be included after the default fields. For example: INFO=<ID=ALLELEID,Number=A,Type=String,Description="Allele ID",Source="ClinVar",Version="20220804"> In the above example, the extra fields of “Source” and “Version” are provided. The values of optional fields must be written as quoted strings, even for numeric values. Other structured lines not defined by this specification may also be used; the only default field for such lines is the required ID field. It is recommended in VCF and required in BCF that the header includes tags describing the reference and contigs backing the data contained in the file. These tags are based on the SQ field from the SAM spec; all tags are optional (see the VCF example above). Meta-information lines are optional, but if they are present then they must be completely well-formed. Other than fileformat, they may appear in any order. Note that BCF, the binary counterpart of VCF, requires that all entries are present. It is recommended to include meta-information lines describing the entries used in the body of the VCF file. 1.4.1 File format A single ‘fileformat’ line is always required, must be the first line in the file, and details the VCF format version number. For VCF version 4.3, this line is: fileformat=VCFv4.3 1.4.2 Information field format INFO fields are described as follows (first four keys are required, source and version are recommended): INFO=<ID=ID,Number=number,Type=type,Description="description",Source="source",Version="version"> Possible Types for INFO fields are: Integer, Float, Flag, Character, and String. The Number entry is an Integer that describes the number of values that can be included with the INFO field. For example, if the INFO field contains a single number, then this value must be 1; if the INFO field describes a pair of numbers, then this value must be 2 and so on. There are also certain special characters used to define special cases: • A: The field has one value per alternate allele. The values must be in the same order as listed in the ALT column (described in section 1.6). • R: The field has one value for each possible allele, including the reference. The order of the values must be the reference allele first, then the alternat