VCF

VCF stands for Variant Call Format, and it is used by the 1000 Genomes project to encode structural genetic variants. See Viewing Variants for example IGV visualizations of mutation and VCF files.

A consistent color sheme is used in the variant display row, which is the top row, for files with or without geneotypes.

Required Extensions: .vcf, .vcf.gz

If the file is gzipped (ends with .vcf.gz), it must have an accompanying Tabix index (see below).

VCF Requirements

IGV supports VCF Version 4.

VCF data files must be indexed for viewing in IGV, either by using igvtools or by using Tabix. 

Load a BAM track for a sample in a VCF file

Display reads associated with a variant genotype in a VCF file by associating BAM files with samples in a VCF file.

Associate BAM files with samples in the VCF file using a 2 column tab-delimited mapping file. 

VCF Specification

Example V.4.0 File:

##fileformat=VCFv4.0
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=1000GenomesPilot-NCBI36
##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=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 NA00003
20 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 0/0:41:3
20 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 2/2:35:4
20 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 0/0:61:2
20 1234567 microsat1 GTCT G,GTACT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3

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.