##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=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##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">
##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element">
##ALT=<ID=CNV,Description="Copy number variable region">
##INFO=<ID=added-genotypes.has_variant,Number=0,Type=Flag,Description="True if added-genotypes has a called alternate among samples under comparison.">
##FORMAT=<ID=added-genotypes,Number=1,Type=String,Description="Genotype from added-genotypes.">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
19	111	.	A	C	9.6	.	added-genotypes.has_variant	GT:HQ:added-genotypes	0|0:10,10:0/0	0|0:10,10:./.	0/1:3,3:0/1
19	112	.	A	G	10	.	added-genotypes.has_variant	GT:HQ:added-genotypes	0|0:10,10:0/0	0|0:10,10:./.	0/1:3,3:0/1
20	14370	rs6054257	G	A	29	PASS	AF=0.5;DP=14;NS=3;DB;H2;added-genotypes.has_variant	GT:GQ:DP:HQ:added-genotypes	0|0:48:1:51,51:0/0	1|0:48:8:51,51:./.	1/1:43:5:.,.:1/1
20	17330	.	T	A	3	q10	AF=0.017;DP=11;NS=3;added-genotypes.has_variant	GT:GQ:DP:HQ:added-genotypes	0|0:49:3:58,50:0/0	0|1:3:5:65,3:./.	0/0:41:3:.,.:0/0
20	1110696	rs6040355	A	G,T	67	PASS	AA=T;AF=0.333,0.667;DP=10;NS=2;DB;added-genotypes.has_variant	GT:GQ:DP:HQ:added-genotypes	1|2:21:6:23,27:1/2	2|1:2:0:18,2:./.	2/2:35:4:.,.:2/2
20	1230237	.	T	.	47	PASS	AA=T;DP=13;NS=3;added-genotypes.has_variant	GT:GQ:DP:HQ:added-genotypes	0|0:54:.:56,60:0/0	0|0:48:4:51,51:./.	0/0:61:2:.,.:0/0
20	1234567	microsat1	G	GA,GAC	50	PASS	AA=G;AC=3,1;AN=6;DP=9;NS=3;added-genotypes.has_variant	GT:GQ:DP:added-genotypes	0/1:.:4:0/1	0/2:17:2:./.	1/1:40:3:1/1
20	1235237	.	T	.	0	.	added-genotypes.has_variant	GT:added-genotypes	0/0:0/0	0|0:./.	./.:.
X	10	rsTest	AC	A,ATG	10	PASS	added-genotypes.has_variant	GT:added-genotypes	0:0	0/1:./.	0|2:0/2