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##fileformat=VCFv4.3
##FILTER=<ID=PASS,Description="All filters passed">
##contig=<ID=11,length=135006516>
##contig=<ID=12,length=135006516>
##FILTER=<ID=flt,Description="Test FILTER">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=XRF,Number=R,Type=Float,Description="Test Number=AGR in INFO">
##INFO=<ID=XAF,Number=A,Type=Float,Description="Test Number=AGR in INFO">
##INFO=<ID=XGF,Number=G,Type=Float,Description="Test Number=AGR in INFO">
##INFO=<ID=XRI,Number=R,Type=Integer,Description="Test Number=AGR in INFO">
##INFO=<ID=XAI,Number=A,Type=Integer,Description="Test Number=AGR in INFO">
##INFO=<ID=XGI,Number=G,Type=Integer,Description="Test Number=AGR in INFO">
##INFO=<ID=XRS,Number=R,Type=String,Description="Test Number=AGR in INFO">
##INFO=<ID=XAS,Number=A,Type=String,Description="Test Number=AGR in INFO">
##INFO=<ID=XGS,Number=G,Type=String,Description="Test Number=AGR in INFO">
##INFO=<ID=ISTR,Number=1,Type=String,Description="Test String in INFO">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=FSTR,Number=1,Type=String,Description="Test String in FORMAT">
##FORMAT=<ID=FFI,Number=1,Type=Integer,Description="Test Integer in FORMAT">
##FORMAT=<ID=FFF,Number=1,Type=Float,Description="Test Float in FORMAT">
##FORMAT=<ID=FAF,Number=A,Type=Float,Description="Test Number=AR in FORMAT">
##FORMAT=<ID=FAI,Number=A,Type=Integer,Description="Test Number=AR in FORMAT">
##FORMAT=<ID=FAS,Number=A,Type=String,Description="Test Number=AR in FORMAT">
##FORMAT=<ID=FRF,Number=R,Type=Float,Description="Test Number=AR in FORMAT">
##FORMAT=<ID=FRI,Number=R,Type=Integer,Description="Test Number=AR in FORMAT">
##FORMAT=<ID=FRS,Number=R,Type=String,Description="Test Number=AR in FORMAT">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Test Number=G in FORMAT">
##INFO=<ID=OLD_REC,Number=1,Type=String,Description="Original variant. Format: CHR|POS|REF|ALT|USED_ALT_IDX">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1 S2 S3 S4
11 101 . G C,* . . OLD_REC=11|101|GCGT|G,GCGA,GTGA,CCGT|4 GT 2 0 0 1
11 101 . GCGT G,* . . OLD_REC=11|101|GCGT|G,GCGA,GTGA,CCGT|1 GT 1 2 2 2
11 102 . C T,* . . OLD_REC=11|101|GCGT|G,GCGA,GTGA,CCGT|3 GT 2 0 1 0
11 104 . T A,* . . OLD_REC=11|101|GCGT|G,GCGA,GTGA,CCGT|2,3 GT 2 1 1 0
11 201 . C G,* . . OLD_REC=11|201|CC|GG,GT|1,2 GT 0 1 1 0
11 202 . C G,* . . OLD_REC=11|201|CC|GG,GT|1 GT 0 1 2 0
11 202 . C T,* . . OLD_REC=11|201|CC|GG,GT|2 GT 0 2 1 0
12 101 rs101 G C,* 199 flt INDEL;AN=4;AC=4,.;DP=19;ISTR=SomeString;XRF=0,4,.;XRI=0,4,.;XRS=000,xx,.;XAF=4,.;XAI=444,.;XAS=zzz,.;OLD_REC=12|101|GCGT|G,GCGA,GTGA,CCGT|4 GT 0/2 2/0 0/0 0/1
12 101 rs101 GCGT G,* 199 flt INDEL;AN=4;AC=1,.;DP=19;ISTR=SomeString;XRF=0,10,.;XRI=0,1111,.;XRS=000,AAA,.;XAF=10,.;XAI=1111,.;XAS=AAA,.;OLD_REC=12|101|GCGT|G,GCGA,GTGA,CCGT|1 GT 0/1 1/2 2/2 2/2
12 102 rs101 C T,* 199 flt INDEL;AN=4;AC=3,.;DP=19;ISTR=SomeString;XRF=0,300000,.;XRI=0,3333,.;XRS=000,DDD,.;XAF=3,.;XAI=33,.;XAS=xx,.;OLD_REC=12|101|GCGT|G,GCGA,GTGA,CCGT|3 GT 0/2 2/0 0/1 0/0
12 104 rs101 T A,* 199 flt INDEL;AN=4;AC=2,.;DP=19;ISTR=SomeString;XRF=0,200,.;XRI=0,2222,.;XRS=000,BBB,.;XAF=200000,.;XAI=22,.;XAS=DDD,.;OLD_REC=12|101|GCGT|G,GCGA,GTGA,CCGT|2,3 GT 0/2 2/1 1/1 1/0
12 201 . C G,* . . OLD_REC=12|201|CC|GG,GT|1,2 GT:FSTR:FFI:FFF:FAF:FAI:FAS:FRF:FRI:FRS:PL 0/0:xx:0:0:1.1,.:1,.:a,.:0,1.1,.:0,1,.:a,b,.:0,1,2,.,.,. 1:yy:11:1.1:1.1,.:1,.:a,.:0,1.1,.:0,1,.:a,b,.:0,2,. 1/1:zz:22:2.2:1.1,.:1,.:a,.:0,1.1,.:0,1,.:a,b,.:0,1,2,.,.,. 0:.:.:.:.,.:.,.:.,.:.:.:.,.,.:.
12 202 . C G,* . . OLD_REC=12|201|CC|GG,GT|1 GT:FSTR:FFI:FFF:FAF:FAI:FAS:FRF:FRI:FRS:PL 0/0:xx:0:0:1.1,.:1,.:a,.:0,1.1,.:0,1,.:a,b,.:0,1,2,.,.,. 1:yy:11:1.1:1.1,.:1,.:a,.:0,1.1,.:0,1,.:a,b,.:0,2,. 2/2:zz:22:2.2:1.1,.:1,.:a,.:0,1.1,.:0,1,.:a,b,.:0,1,2,.,.,. 0:.:.:.:.,.:.,.:.,.:.:.:.,.,.:.
12 202 . C T,* . . OLD_REC=12|201|CC|GG,GT|2 GT:FSTR:FFI:FFF:FAF:FAI:FAS:FRF:FRI:FRS:PL 0/0:xx:0:0:2.2,.:2,.:b,.:0,2.2,.:0,2,.:a,c,.:0,3,5,.,.,. 2:yy:11:1.1:2.2,.:2,.:b,.:0,2.2,.:0,2,.:a,c,.:0,5,. 1/1:zz:22:2.2:2.2,.:2,.:b,.:0,2.2,.:0,2,.:a,c,.:0,3,5,.,.,. 0:.:.:.:.,.:.,.:.,.:.:.:.,.,.:.
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