VCF stands for Variant Call Format, and it is used by the 1000 Genomes project to encode structural genetic variants.
Required Extensions: .vcf, .vcf.gz
If the file is gzipped (ends with .vcf.gz), it must have an accompanying Tabix index (see below).
The version 4.0 spec: http://www.1000genomes.org/wiki/doku.php?id=1000_genomes:analysis:vcf4.0
Example V.4.0 File:
This example shows in order:
Genotype data are given for three samples, two of which are phased and the third unphased, with per sample genotype quality, depth, and haplotype qualities (the latter only for the phased samples) given as well as the genotypes. The microsatellite calls are unphased.
IGV supports VCF Version 4.
VCF data files must be indexed for viewing in IGV, either by using igvtools or by using Tabix.