##fileformat=VCFv4.0
##problem1=The first base of the second ALT allele at 20:1234567 does not match the reference.
##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=-1,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=-1,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
19	111	.	A	C	9.6	.	.	GT:HQ	0|0:10,10	0|0:10,10	0\1:3,3
19	112	.	A	G	10	.	.	GT:HQ	0|0:10,10	0|0:10,10	0\1:3,3
20	14370	rs6054257	G	A	29	0	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:-1,-1
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:-1,-1
20	1110696	rs6040355	A	G,T	67	0	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:-1,-1
20	1230237	.	T	.	47	0	NS=3;DP=13;AA=T	GT:GQ:DP:HQ	0|0:54:-1:56,60	0|0:48:4:51,51	0/0:61:2:-1,-1
20	1234567	microsat1	G	GA,AAC	50	0	NS=3;DP=9;AA=G;AN=6;AC=3,1	GT:GQ:DP	0/1:-1:4	0/2:17:2	1/1:40:3
20	1235237	.	T	.	-1	.	.	GT	0\0	0|0	./.
X	10	rsTest	AC	A,ATG	10	.	.	GT	0	0/1	0|2
X	11	rsTest2	T	A,G	10	q10;s50	.	GT:DP:GQ	0:3:10	.:5:20	0:3:10
