VCF format

VCF (Variant call 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.

Example

##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">
#CHROM POS     ID        REF ALT    QUAL FILTER INFO
20     14370   rs6054257 G      A       29   PASS   NS=3;DP=14;AF=0.5;DB;H2
20     17330   .         T      A       3    q10    NS=3;DP=11;AF=0.017
20     1110696 rs6040355 A      G,T     67   PASS   NS=2;DP=10;AF=0.333,0.667;AA=T;DB
20     1230237 .         T      .       47   PASS   NS=3;DP=13;AA=T
20     1234567 microsat1 GTCT   G,GTACT 50   PASS   NS=3;DP=9;AA=G

References

1. VCF (Variant Call Format) version 4.0