Variant Calling Format

VCF is a text file format (most likely stored in a compressed manner). It contains meta-information lines, a header line, and then data lines each containing information about a position in the genome. The format also has the ability to contain genotype information on samples for each position. File meta-information is included after the ## string, often as key=value pairs. For example: ##fileformat=VCFv4.2. The header line names the 8 fixed, mandatory columns: #CHROM POS ID REF ALT QUAL FILTER INFO. If genotype data is present in the file, these are followed by a FORMAT column header, then an arbitrary number of sample IDs. Duplicate sample IDs are not allowed. The header line is tab-delimited. There is an example:

##fileformat=VCFv4.2
##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    POSID    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