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Variant Call Format

The Variant Call Format or VCF is a standard text file format used in bioinformatics for storing gene sequence or DNA 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 4.5,[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]

Example

##fileformat=VCFv4.3##fileDate=20090805##source=myImputationProgramV3.1##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>##phasing=partial##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">##FILTER=<ID=q10,Description="Quality below 10">##FILTER=<ID=s50,Description="Less than 50% of samples have data">##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA0000320 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 0/0:41:320 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 2/2:35:420 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 0/0:61:220 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
BCF v VCF
Demonstrating the difference between the binary BCF and VCF formats.

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 fileformat, fileDate and reference.

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):[6]

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

References

  1. ^ a b Danecek, 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.
  2. ^ Ossola, Alexandra (20 March 2015). "The Race to Build a Search Engine for Your DNA". IEEE Spectrum. Retrieved 22 March 2015.
  3. ^ "Understanding VCF format | Human genetic variation". EMBL-EBI. Archived from the original on 2023-04-20. Retrieved 2023-11-10.
  4. ^ 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.
  5. ^ 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.
  6. ^ a b "VCF Specification" (PDF). Retrieved 30 July 2024.
  7. ^ "Specifications of SAM/BAM and related high-throughput sequencing file formats". GitHub. Retrieved 24 June 2014.
  8. ^ "Encoding Structural Variants in VCF (Variant Call Format) version 4.0 | 1000 Genomes". Retrieved 20 October 2016.
  9. ^ "GVCF - Genomic Variant Call Format". GATK. Broad Institute.
  10. ^ "gVCF Files". Illumina, Inc. Retrieved 2023-11-10.
  11. ^ "HTS format specifications". samtools.github.io. Retrieved 2022-02-22.
  12. ^ "Bio-IT World". www.bio-itworld.com. Retrieved 2018-10-26.

External links