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.

The standard is currently in version 4.2,[1][2] 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.[3] A set of tools is also available for editing and manipulating the files.[4]

Example[edit]

##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

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