##fileformat=VCFv4.1
##fileDate=20090805
##source=myImputationProgramV3.1
##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=A,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">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##FILTER=<ID=q10,Description="Quality below 10 (\"with quotes\")">
##FILTER=<ID=s50,Description="Less than 50% of samples have data (with \\ backslash)">
##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">
##FORMAT=<ID=GL,Number=G,Type=Integer,Description="Genotype Likelihood">
##reference=file:/lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
##contig=<ID=19,length=59128983,md5=1aacd71f30db8e561810913e0b72636d,species="Homo Sapiens">
##contig=<ID=20,length=63025520,md5=0dec9660ec1efaaf33281c0d5ea2560f,species="Homo Sapiens">
##contig=<ID=Y,length=63025520,md5=0dec9660ec1efaaf33281c0d5ea2560f,species="Homo Sapiens">
##SAMPLE=<ID=Blood,Genomes=Germline,Mixture=1.,Description="Patient germline genome">
##SAMPLE=<ID=TissueSample,Genomes=Germline;Tumor,Mixture=.3;.7,Description="Patient germline genome;Patient tumor genome">
##PEDIGREE=<Derived=ID2,Original=ID1>
##PEDIGREE=<Child=CHILD-GENOME-ID,Mother=MOTHER-GENOME-ID,Father=FATHER-GENOME-ID>
##pedigreeDB=url
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
19	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	GTC	G,GTCTC	50	PASS	NS=3;DP=9;AA=G	GT:GQ:DP	0/1:35:4	0/2:17:2	1/1:40:3
20	2234567	.	C	[13:123457[ACGC	50	PASS	SVTYPE=BND;NS=3;DP=9;AA=G	GT:GQ:DP	0/1:35:4	0/1:17:2	1/1:40:3
20	2234568	.	C	.TC	50	PASS	SVTYPE=BND;NS=3;DP=9;AA=G	GT:GQ:DP	0/1:35:4	0/1:17:2	1/1:40:3
20	2234569	.	C	CT.	50	PASS	SVTYPE=BND;NS=3;DP=9;AA=G	GT:GQ:DP	0/1:35:4	0/1:17:2	1/1:40:3
20	3234569	.	C	<INV>	50	PASS	SVTYPE=BND;NS=3;DP=9;AA=G	GT:GQ:DP	0/1:35:4	0/1:17:2	1/1:40:3
20	4234569	.	N	.[13:123457[	50	PASS	SVTYPE=BND;NS=3;DP=9;AA=G	GT:GQ:DP	0/1:35:4	0/1:17:2	./.:40:3
20	5234569	.	N	[13:123457[.	50	PASS	SVTYPE=BND;NS=3;DP=9;AA=G	GT:GQ:DP	0/1:35:4	0/1:17:2	1/1:40:3
Y	17330	.	T	A	3	q10	NS=3;DP=11;AF=0.017	GT:GL	0:0,49	0:0,3	1:41,0