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##fileformat=VCFv4.1
##fileDate=20110603
##source=myImputationProgramV4.1
##reference=file:/seq/references/reference.fasta
##phasing=partial
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=MATEID,Number=1,Type=String,Description="ID of the mate breakend">
##INFO=<ID=REVERSE,Number=0,Type=Flag,Description="Indicates a breakend on the 5' end of a reference segment">
##INFO=<ID=MATEPOS,Number=1,Type=Integer,Description="Position of the mate breakend">
##INFO=<ID=MATECHR,Number=1,Type=String,Description="Chromosome containing the mate breakend">
##INFO=<ID=SVLEN,Number=-1,Type=Integer,Description="Length of ALT alleles">
##INFO=<ID=CN,Number=-1,Type=Integer,Description="Copy number of segment containing breakend">
##INFO=<ID=CNADJ,Number=-1,Type=Integer,Description="Copy number of adjacency">
##FILTER=<ID=q10,Description="Quality below 10">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=G,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=G,Type=Integer,Description="Read Depth">
##FORMAT=<ID=HQ,Number=G,Type=Integer,Description="Haplotype Quality">
##FORMAT=<ID=BHAP,Number=G,Type=String,Description="Bundle Phase Set ">
##FORMAT=<ID=BCN,Number=G,Type=String,Description="Bundle copy number">
##PEDIGREE=<Derived="Tumor",Original="Germline">
##SAMPLE=<SampleName=<GermlineS>,Genomes=<Germline>,Mixture=<1.0>,Description=<"Germline genome"> >
##SAMPLE=<SampleName=<TumorS>,Genomes=<Germline,Tumor>,Mixture=<0.1,0.9>,Description=<"Germline contamination","Tumor genome"> >
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Germline Tumor
1 2 snp1 A T 40 PASS GT:MQ:HAP 0|1:0,40:35,46 0|1:0,0:35,46
1 2 bnd1 T T[2:3[ 40 PASS SVTYPE=BND;MATEID=bnd4 GT:MQ:BHAP 0|0:0,0:35>35,46>46 0|1:0,40:35>35,46>17
1 3 bnd2 A ]2:2]A 40 PASS SVTYPE=BND;MATEID=bnd3 GT:MQ:BHAP 0|0:0,0:35>35,46>46 0|1:0,40:35>35,46>17
2 1 snp2 G T 40 PASS GT:MQ:HAP 1|0:0,40:17,23 1|0:0,0:17,23
2 2 bnd3 G G[1:3[ 40 PASS SVTYPE=BND;MATEID=bnd2 GT:MQ:BHAP:BCN 0|0:0,0:17>17,23>23:1,1 0|1:0,40:23>23,17>46:2,1
2 3 bnd4 G ]1:2]G 40 PASS SVTYPE=BND;MATEID=bnd1 GT:MQ:BHAP:BCN 0|0:0,0:17>17,23>23:1,1 0|1:0,40:23>23,17>46:2,1
2 4 bnd5 G ]2:6]G 40 PASS SVTYPE=BND;MATEID=bnd6 GT:MQ:BHAP:AHAP:BCN 0|0:0,0:17>17,23>23:17,23:1,1 0|0|1:0,0,40:17>17,23>23,24>23:17,23,23:1,2,2
2 6 bnd6 T T[2:4[ 40 PASS SVTYPE=BND;MATEID=bnd5 GT:MQ:BHAP:AHAP:BCN 0|0:0,0:17>17,23>23:17,23:1,1 0|1|0:0,40,0:17>17,23>24,24>24:17,23,23:1,2,2
2 6 snp3 T A 40 PASS GT:MQ:HAP:AHAP 0|1:0,40:23,17:23,17 0|1|1:0,0,0:17,23,24:17,23,23
2 8 snp4 T A 40 PASS GT:MQ:HAP:AHAP 0|0:0,0:23,17:23,17 0|1|1:0,40,40:17,23,24:17,23,23
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