Trisha Shetty (Editor)

Variant Call Format

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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.

Contents

The standard is currently in version 4.3, although the 1000 Genomes Project has developed their own specification for structural variations such as duplications, which are not easily accommodated into the existing schema. A set of tools is also available for editing and manipulating the files.

Example

##fileformat=VCFv4.0 ##fileDate=20110705 ##reference=1000GenomesPilot-NCBI37 ##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=.,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=GQ,Number=1,Type=Integer,Description="Genotype Quality"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##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 Sample1 Sample2 Sample3 2 4370 rs6057 G A 29 . NS=2;DP=13;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:52,51 1|0:48:8:51,51 1/1:43:5:.,. 2 7330 . T A 3 q10 NS=5;DP=12;AF=0.017 GT:GQ:DP:HQ 0|0:46:3:58,50 0|1:3:5:65,3 0/0:41:3 2 110696 rs6055 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 2 130237 . T . 47 . NS=2;DP=16;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:56,51 0/0:61:2 2 134567 microsat1 GTCT G,GTACT 50 PASS NS=2;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3 chr1 45796269 . G C chr1 45797505 . C G chr1 45798555 . T C chr1 45798901 . C T chr1 45805566 . G C chr2 47703379 . C T chr2 48010488 . G A chr2 48030838 . A T chr2 48032875 . CTAT - chr2 48032937 . T C chr2 48033273 . TTTTTGTTTTAATTCCT - chr2 48033551 . C G chr2 48033910 . A T chr2 215632048 . G T chr2 215632125 . TT - chr2 215632155 . T C chr2 215632192 . G A chr2 215632255 . CA TG chr2 215634055 . C T

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 of 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):

AA 
ancestral allele
AC 
allele count in genotypes, for each ALT allele, in the same order as listed
AF 
allele frequency for each ALT allele in the same order as listed: use this when estimated from primary data, not called genotypes
AN 
total number of alleles in called genotypes
BQ 
RMS base quality at this position
CIGAR 
cigar string describing how to align an alternate allele to the reference allele
DB 
dbSNP membership
DP 
combined depth across samples, e.g. DP=154
END 
end position of the variant described in this record (for use with symbolic alleles)
H2 
membership in hapmap2
H3 
membership in hapmap3
MQ 
RMS mapping quality, e.g. MQ=52
MQ0 
Number of MAPQ == 0 reads covering this record
NS 
Number of samples with data
SB 
strand bias at this position
SOMATIC 
indicates that the record is a somatic mutation, for cancer genomics
VALIDATED 
validated by follow-up experiment
1000G 
membership in 1000 Genomes

References

Variant Call Format Wikipedia
(Text) CC BY-SA