Variant Call Format (VCF) is a text file format for storing marker and genotype data. This short tutorial describes how Variant Call Format encodes data for single nucleotide variants.
Every VCF file has three parts in the following order:
Each VCF record has the same number of tab-separated fields as the header line. The symbol "." is used to denote missing data.
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Each meta-information line must have the form ##KEY=VALUE and cannot contain white-space. The first meta-information line must specify the VCF version number (version 4.2 in the example). Additional meta-information lines are optional, but are often included to describe terms used in the FILTER, INFO, and FORMAT fields. In the example, the additional meta-information lines say that that GT means genotype, GP means the probability of each possible genotype call, and GL means the likelihood of each possible genotype call.
The first nine columns of the header line and data lines describe the variants:
| CHROM | the chromosome. |
| POS | the genome coordinate of the first base in the variant. Within a chromosome, VCF records are sorted in order of increasing position. |
| ID | a semicolon-separated list of marker identifiers. |
| REF | the reference allele expressed as a sequence of one or more A/C/G/T nucleotides (e.g. "A" or "AAC") |
| ALT | the alternate allele expressed as a sequence of one or more A/C/G/T nucleotides (e.g. "A" or "AAC"). If there is more than one alternate alleles, the field should be a comma-separated list of alternate alleles. |
| QUAL | probability that the ALT allele is incorrectly specified, expressed on the the phred scale (-10log10(probability)). |
| FILTER | Either "PASS" or a semicolon-separated list of failed quality control filters. |
| INFO | additional information (no white space, tabs, or semi-colons permitted). |
| FORMAT | colon-separated list of data subfields reported for each sample. The format fields in the Example are explained below. |
After the nine fixed columns, the remaining columns contain the sample identifier and the colon-separated data subfields for each individual. The data subfields in a record must match that record's format subfields.
The most common format subfield is GT (genotype) data. If the GT subfield is present, it must be the first subfield. In the sample data, genotype alleles are numeric: the REF allele is 0, the first ALT allele is 1, and so on. The allele separator is '/' for unphased genotypes and '|' for phased genotypes. In the example, all genotypes are unphased, and the genotypes for SAMP001 are homozygote reference, heterozygote, and missing in the first, second, and third records.
The second record contains a GP(genotype probability) format subfield, and the third record contains PL (phred-scaled genotype likelihood) format subfield. GP and GL data subfields are three comma-separated values corresponding to the REF/REF, REF/ALT, and ALT/ALT genotypes in that order. To convert a phred-scaled likelihood P to a raw likelihood L, use the formula L = 10(-P/10).
In the second record of the Example, the GP data subfield is missing for SAMP001 and the GP subfield for SAMP002 has probabilities of 0.03, 0.97, and 0 for the REF/REF, REF/ALT, and ALT/ALT genotypes.
In the third record of the Example, the GL data subfield is missing for SAMP001. The GL subfield for SAMP002 has phred-scaled likelihoods of 10, 5, and 0 and raw likelihoods of 0.1, 0.316, and 1 for the REF/REF, REF/ALT, and ALT/ALT genotypes. It is not necessary for the genotype likelihoods to sum to 1.0.
Here are some tools for manipulating VCF files:
If you need to encode more complicated genotype data or if you want to learn more about Variant Call Format, see the VCF 4.2 specification.
Prepared by Steven Smith and Brian Browning
Last updated: 29 Sept 2014.