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 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.

Example

##fileformat=VCFv4.3
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
##contig=
##phasing=partial
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##FILTER=
##FILTER=
##FORMAT=
##FORMAT=
##FORMAT=
##FORMAT=
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0, 0:48:1:51,51 1, 0:48:8:51,51 1/1:43:5:.,.
20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0, 0:49:3:58,50 0, 1:3:5:65,3 0/0:41:3
20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1, 2:21:6:23,27 2, 1:2:0:18,2 2/2:35:4
20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0, 0:54:7:56,60 0, 0:48:4:51,51 0/0:61:2
20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3

The VCF header

The header begins the file and provides metadata describing the body of the file. Header lines are denoted as starting with . Special keywords in the header are denoted with . Recommended keywords include , and .

The header contains keywords that optionally semantically and syntactically describe the fields used in the body of the file, notably INFO, FILTER, and FORMAT (see below).

The columns of a VCF

The body of VCF follows the header, and is tab separated into 8 mandatory columns and an unlimited number of optional columns that may be used to record other information about the sample(s). When additional columns are used, the first optional column is used to describe the format of the data in the columns that follow.

Common INFO fields

Arbitrary keys are permitted, although the following sub-fields are reserved (albeit optional):

Any other info fields are defined in the .vcf header.

Common FORMAT fields

Any other format fields are defined in the .vcf header.

See also

* The FASTA format, used to represent genome sequences.
* The FASTQ format, used to represent DNA sequencer reads along with quality scores.
* The SAM format, used to represent genome sequencer reads that have been aligned to genome sequences.
* The GVF format (Genome Variation Format), an extension based on the GFF3 format.

* Global Alliance for Genomics and Health (GA4GH), the group leading the management and expansion of the VCF format. The VCF specification is no longer maintained by the 1000 Genomes Project.

* Human genome
* Human genetic variation
* Single Nucleotide Polymorphism (SNP)

References

External links

An explanation of the format in picture form
*

{{Bioinformatics

Biological sequence format