#VCF_test
#from http://www.sph.umich.edu/csg/liyanmin/vcfCodingSnps/Tutorial.shtml
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA12891 NA12892
1	3	.	A	G	50	depth=20	ANNO=Normal_Splice_Site:GENE1|GENE3;ANNOFULL=GENE1/CODING_GENE:+:Normal_Splice_Site:Utr5:Exon|GENE3/CODING_GENE:-:Normal_Splice_Site:Utr3:Exon|GENE2/NON_CODING_GENE:+:Upstream	GT:GQ:GD	1/0:31:12	0/0:28:14
1	5	.	C	A	50	depth=20	ANNO=Nonsynonymous:GENE1|GENE3;ANNOFULL=GENE1/CODING_GENE:+:Nonsynonymous(CCT/Pro/P->CAT/His/H:Base3/30:Codon1/10:Exon1/5):Normal_Splice_Site:Exon|GENE3/CODING_GENE:-:Nonsynonymous(AGG/Arg/R->ATG/Met/M:Base30/30:Codon10/10:Exon5/5):Normal_Splice_Site:Exon|GENE2/NON_CODING_GENE:+:Upstream	GT:GQ:GD	1/0:31:12	0/0:28:14
1	7	.	TAA	.	50	depth=20	ANNO=Monomorphic;ANNOFULL=Monomorphic	GT:GQ:GD	1/0:31:12	0/0:28:14
1	13	.	T	G	50	depth=20	ANNO=Synonymous:GENE1|GENE3;ANNOFULL=GENE1/CODING_GENE:+:Synonymous(CCT/Pro/P->CCG/Pro/P:Base4/30:Codon2/10:Exon2/5):Normal_Splice_Site:Exon|GENE3/CODING_GENE:-:Synonymous(AGG/Arg/R->CGG/Arg/R:Base29/30:Codon10/10:Exon4/5):Normal_Splice_Site:Exon|GENE2/NON_CODING_GENE:+:Upstream;REGION=c	GT:GQ:GD	1/0:31:12	0/0:28:14
1	14	.	A	AGCG	50	depth=20	ANNO=CodonGain:GENE1|GENE3;ANNOFULL=GENE1/CODING_GENE:+:CodonGain(Ala):Insertion:Normal_Splice_Site:Exon|GENE3/CODING_GENE:-:CodonGain(Arg):Insertion:Normal_Splice_Site:Exon|GENE2/NON_CODING_GENE:+:Insertion:Upstream;REGION=c	GT:GQ:GD	1/0:31:12	0/0:28:14
1	20	.	AAGTA	A	50	depth=20	ANNO=Frameshift:GENE1|GENE3;ANNOFULL=GENE1/CODING_GENE:+:Frameshift:Deletion:Essential_Splice_Site:Normal_Splice_Site:Exon:Intron|GENE3/CODING_GENE:-:Frameshift:Deletion:Essential_Splice_Site:Normal_Splice_Site:Exon:Intron|GENE2/NON_CODING_GENE:+:Deletion:Normal_Splice_Site:Exon:Noncoding	GT:GQ:GD	1/0:31:12	0/0:28:14
1	22	.	G	GC	50	depth=20	ANNO=Insertion:GENE1|GENE2|GENE3;ANNOFULL=GENE1/CODING_GENE:+:Insertion:Essential_Splice_Site:Intron|GENE3/CODING_GENE:-:Insertion:Essential_Splice_Site:Intron|GENE2/NON_CODING_GENE:+:Insertion:Normal_Splice_Site:Exon:Noncoding;REGION=f	GT:GQ:GD	1/0:31:12	0/0:28:14
1	25	.	A	C	50	depth=20	ANNO=Stop_Loss:GENE1;ANNOFULL=GENE1/CODING_GENE:+:Stop_Loss(TAA/Stp/O->TAC/Tyr/Y:Base10/30:Codon4/10:Exon3/5):Normal_Splice_Site:Exon|GENE3/CODING_GENE:-:Nonsynonymous(TTA/Leu/L->GTA/Val/V:Base23/30:Codon8/10:Exon3/5):Normal_Splice_Site:Exon|GENE2/NON_CODING_GENE:+:Normal_Splice_Site:Exon:Noncoding;REGION=f	GT:GQ:GD	1/0:31:12	0/0:28:14
1	43	.	C	A	50	depth=20	ANNO=Normal_Splice_Site:GENE1|GENE3;ANNOFULL=GENE1/CODING_GENE:+:Normal_Splice_Site:Intron|GENE3/CODING_GENE:-:Normal_Splice_Site:Intron|GENE2/NON_CODING_GENE:+:Downstream;REGION=f	GT:GQ:GD	1/0:31:12	0/0:28:14
1	44	.	T	G	50	depth=20	ANNO=Normal_Splice_Site:GENE1|GENE3;ANNOFULL=GENE1/CODING_GENE:+:Normal_Splice_Site:Intron|GENE3/CODING_GENE:-:Normal_Splice_Site:Intron|GENE2/NON_CODING_GENE:+:Downstream;REGION=f	GT:GQ:GD	1/0:31:12	0/0:28:14
1	50	.	A	C	50	depth=20	ANNO=Essential_Splice_Site:GENE1|GENE3;ANNOFULL=GENE1/CODING_GENE:+:Essential_Splice_Site:Intron|GENE3/CODING_GENE:-:Essential_Splice_Site:Intron|GENE2/NON_CODING_GENE:+:Downstream;REGION=f,e	GT:GQ:GD	1/0:31:12	0/0:28:14
1	53	.	C	A[	50	depth=20	ANNO=StructuralVariation:GENE1|GENE2|GENE3;ANNOFULL=GENE1/CODING_GENE:+:StructuralVariation:CodonRegion:Normal_Splice_Site:Exon|GENE3/CODING_GENE:-:StructuralVariation:CodonRegion:Normal_Splice_Site:Exon|GENE2/NON_CODING_GENE:+:StructuralVariation:Downstream;REGION=f,e	GT:GQ:GD	1/0:31:12	0/0:28:14	
1	53	.	C	A	50	depth=20	ANNO=Nonsynonymous:GENE1;ANNOFULL=GENE1/CODING_GENE:+:Nonsynonymous(CCC/Pro/P->ACC/Thr/T:Base20/30:Codon7/10:Exon5/5):Normal_Splice_Site:Exon|GENE3/CODING_GENE:-:Synonymous(GGG/Gly/G->GGT/Gly/G:Base13/30:Codon5/10:Exon1/5):Normal_Splice_Site:Exon|GENE2/NON_CODING_GENE:+:Downstream;REGION=f,e	GT:GQ:GD	1/0:31:12	0/0:28:14
1	53	.	C	A,T	50	depth=20	ANNO=Nonsynonymous:GENE1;ANNOFULL=GENE1/CODING_GENE:+:Nonsynonymous(CCC/Pro/P->ACC/Thr/T:Base20/30:Codon7/10:Exon5/5):Normal_Splice_Site:Exon|GENE3/CODING_GENE:-:Synonymous(GGG/Gly/G->GGT/Gly/G:Base13/30:Codon5/10:Exon1/5):Normal_Splice_Site:Exon|GENE2/NON_CODING_GENE:+:Downstream;REGION=f,e	GT:GQ:GD	1/0:31:12	0/0:28:14	
1	66	.	T	C	50	depth=20	ANNO=Utr5:GENE3;ANNOFULL=GENE1/CODING_GENE:+:Utr3:Exon|GENE3/CODING_GENE:-:Utr5:Exon|GENE2/NON_CODING_GENE:+:Downstream;REGION=f,e	GT:GQ:GD	1/0:31:12	0/0:28:14
1	72	.	C	A	50	depth=20	ANNO=Upstream:GENE3;ANNOFULL=GENE1/CODING_GENE:+:Downstream|GENE3/CODING_GENE:-:Upstream|GENE2/NON_CODING_GENE:+:Downstream;REGION=f,e	GT:GQ:GD	1/0:31:12	0/0:28:14
1	2000	.	C	A	50	depth=20	ANNO=Intergenic;ANNOFULL=Intergenic	GT:GQ:GD	1/0:31:12	0/0:28:14
