Possible Types for FORMAT fields are: Integer, Float, Character, and String. Likewise, Genotype fields specified in the FORMAT field should be described as follows: The Description value must be surrounded by double-quotes.įILTERs that have been applied to the data should be described as follows:
The ‘Flag’ type indicates that the INFO field does not contain a Value entry, and hence the Number should be 0 in this case. Possible Types are: Integer, Float, Character, String and Flag. If the number of possible values varies, is unknown, or is unbounded, then this value should be ‘.’. However, if the INFO field describes a pair of numbers, then this value should be 2 and so on. For example, if the INFO field contains a single number, then this value should be 1. The Number entry is an Integer that describes the number of values that can be included with the INFO field. Possible Types for INFO fields are: Integer, Float, Flag, Character, and String. INFO fields should be described as follows (all keys are required): Although they are optional, if these lines are present then they must be completely well-formed. It is strongly encouraged that information lines describing the INFO, FILTER and FORMAT entries used in the body of the VCF file be included in the meta-information section. For example, for VCF version 4.0, this line should read: The ‘fileformat’ field is always required and should detail the VCF format version number. Meta-information linesįile meta-information is included after the # string, often as key=value pairs. Genotype data are given for three samples, two of which are phased and the third unphased, with per sample genotype quality, depth and haplotype qualities (the latter only for the phased samples) given as well as the genotypes. with no alternate alleles), and a microsatellite with two alternative alleles, one a deletion of 3 bases (TCT), and the other an insertion of one base (A). This example shows in order a good simple SNP, a possible SNP that has been filtered out because its quality is below 10, a site at which two alternate alleles are called, with one of them (T) being ancestral (possibly a reference sequencing error), a site that is called monomorphic reference (i.e. There is an option whether to contain genotype information on samples for each position or not. It contains meta-information lines, a header line, and then data lines each containing information about a position in the genome. VCF is a text file format (most likely stored in a compressed manner). Please see VCF_4.0_sv for the conventions and extensions adopted by the 1000 Genomes Project for encoding structural variations in VCF 4.0 format. Details of the current version can be found with the HTS specifications. The VCF specification is now maintained by GA4GH.
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