This article is about the bioinformatics text file format. For the virtual contact file format, see vCard.
Variant Call Format
Filename extension
.vcf
Developed by
1000 Genomes Project
Latest release
4.3 January 13, 2021; 3 years ago (2021-01-13)
Type of format
Bioinformatics
Extended from
Tab-separated values
Extended to
gVCF
Open format?
Yes
Website
samtools.github.io/hts-specs/VCFv4.3.pdf
The Variant Call Format (VCF) is a standard text file format used in bioinformatics for storing gene sequence variations. The format was developed in 2010 for the 1000 Genomes Project and has since been used by other large-scale genotyping and DNA sequencing projects.[1][2] VCF is a common output format for variant calling programs due to its relative simplicity and scalability.[3][4] Many tools have been developed for editing and manipulating VCF files, including VCFtools, which was released in conjunction with the VCF format in 2011, and BCFtools, which was included as part of SAMtools until being split into an independent package in 2014.[1][5]
The standard is currently in version 4.3,[6][7] 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.[8]
Additional file formats have been developed based on VCF, including genomic VCF (gVCF). gVCF is an extended format which includes additional information about "blocks" that match the reference and their qualities.[9][10]
^ abDanecek, Petr; Auton, Adam; Abecasis, Goncalo; Albers, Cornelis A.; Banks, Eric; DePristo, Mark A.; Handsaker, Robert E.; Lunter, Gerton; Marth, Gabor T.; Sherry, Stephen T.; McVean, Gilean; Durbin, Richard (2011-08-01). "The variant call format and VCFtools". Bioinformatics. 27 (15): 2156–2158. doi:10.1093/bioinformatics/btr330. ISSN 1367-4803. PMC 3137218. PMID 21653522.
^Ossola, Alexandra (20 March 2015). "The Race to Build a Search Engine for Your DNA". IEEE Spectrum. Retrieved 22 March 2015.
^"Understanding VCF format | Human genetic variation". EMBL-EBI. Archived from the original on 2023-04-20. Retrieved 2023-11-10.
^Garrison, Erik; Kronenberg, Zev N.; Dawson, Eric T.; Pedersen, Brent S.; Prins, Pjotr (2022-05-31). "A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar". PLOS Computational Biology. 18 (5): e1009123. Bibcode:2022PLSCB..18E9123G. doi:10.1371/journal.pcbi.1009123. ISSN 1553-734X. PMC 9286226. PMID 35639788.
^Danecek, Petr; Bonfield, James K; Liddle, Jennifer; Marshall, John; Ohan, Valeriu; Pollard, Martin O; Whitwham, Andrew; Keane, Thomas; McCarthy, Shane A; Davies, Robert M; Li, Heng (2021-01-29). "Twelve years of SAMtools and BCFtools". GigaScience. 10 (2). doi:10.1093/gigascience/giab008. ISSN 2047-217X. PMC 7931819. PMID 33590861.
^"VCF Specification" (PDF). Retrieved 20 Oct 2016.
^"Specifications of SAM/BAM and related high-throughput sequencing file formats". GitHub. Retrieved 24 June 2014.
^"Encoding Structural Variants in VCF (Variant Call Format) version 4.0 | 1000 Genomes". Retrieved 20 October 2016.
^"GVCF - Genomic Variant Call Format". GATK. Broad Institute.
^"gVCF Files". Illumina, Inc. Retrieved 2023-11-10.
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