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Adding as many test data files into public/testdata as possible
2012-05-23 04:26:28 +08:00
##fileformat=VCFv4.0
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=DBSNP129,Number=0,Type=Flag,Description="DBSNP129 Membership">
##INFO=<ID=DBSNP132,Number=0,Type=Flag,Description="DBSNP132 Membership">
##INFO=<ID=GenericAnnotation,Number=1,Type=Integer,Description="For each variant in the 'variants' ROD, finds all entries in the other -B files that overlap the variant's position.">
##INFO=<ID=HAPMAP,Number=0,Type=Flag,Description="HAPMAP Membership">
##INFO=<ID=OMNI,Number=0,Type=Flag,Description="OMNI Membership">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00513 NA12045 HG00625
20 10003358 rs926982 A C 92318.04 PASS AC=5;AF=0.83;AN=6;DBSNP129;DBSNP132;DP=7 GT:DP:GQ:PL 1/1:1:3:34,3,0 0/1:5:51:51,0,95 1/1:1:3:27,3,0
20 10003692 rs2064653 A G 119873.04 PASS AC=5;AF=0.83;AN=6;DBSNP129;DBSNP132;DP=9 GT:DP:GQ:PL 1/1:2:6:66,6,0 0/1:4:20:20,0,85 1/1:3:9:112,9,0
20 10015679 rs113024248 C . 2829.33 PASS AC=0;AF=0.00;AN=0;DBSNP132;DP=0;OMNI GT:DP:PL ./. ./. ./.
20 10015790 rs114356776 G . 43.60 PASS AC=0;AF=0.00;AN=0;DBSNP132;DP=0;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.-300G>A;refseq.codingCoordStr_2=c.-236G>A;refseq.codingCoordStr_3=c.-300G>C;refseq.codingCoordStr_4=c.-236G>C;refseq.codingCoordStr_5=c.-300G>G;refseq.codingCoordStr_6=c.-236G>G;refseq.codingCoordStr_7=c.-300G>T;refseq.codingCoordStr_8=c.-236G>T;refseq.end_1=10015790;refseq.end_2=10015790;refseq.end_3=10015790;refseq.end_4=10015790;refseq.end_5=10015790;refseq.end_6=10015790;refseq.end_7=10015790;refseq.end_8=10015790;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=94;refseq.mrnaCoord_2=94;refseq.mrnaCoord_3=94;refseq.mrnaCoord_4=94;refseq.mrnaCoord_5=94;refseq.mrnaCoord_6=94;refseq.mrnaCoord_7=94;refseq.mrnaCoord_8=94;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr5;refseq.positionType_2=utr5;refseq.positionType_3=utr5;refseq.positionType_4=utr5;refseq.positionType_5=utr5;refseq.positionType_6=utr5;refseq.positionType_7=utr5;refseq.positionType_8=utr5;refseq.spliceDist_1=94;refseq.spliceDist_2=94;refseq.spliceDist_3=94;refseq.spliceDist_4=94;refseq.spliceDist_5=94;refseq.spliceDist_6=94;refseq.spliceDist_7=94;refseq.spliceDist_8=94;refseq.start_1=10015790;refseq.start_2=10015790;refseq.start_3=10015790;refseq.start_4=10015790;refseq.start_5=10015790;refseq.start_6=10015790;refseq.start_7=10015790;refseq.start_8=10015790;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+ GT:DP:PL ./. ./. ./.
20 10019093 rs575534 A G 69795.04 PASS AC=3;AF=0.50;AN=6;DBSNP129;DBSNP132;DP=14;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=20;refseq.chr_2=20;refseq.codingCoordStr_1=c.144A>G;refseq.codingCoordStr_2=c.144A>G;refseq.codonCoord_1=48;refseq.codonCoord_2=48;refseq.end_1=10019093;refseq.end_2=10019093;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=537;refseq.mrnaCoord_2=473;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G48G;refseq.proteinCoordStr_2=p.G48G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGA;refseq.referenceCodon_2=GGA;refseq.spliceDist_1=188;refseq.spliceDist_2=188;refseq.start_1=10019093;refseq.start_2=10019093;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG GT:DP:GQ:PL 0/1:3:24:24,0,60 0/0:6:18:0,18,211 1/1:5:15:172,15,0
20 10019169 rs7260784 C . 1193.61 PASS AC=0;AF=0.00;AN=6;DBSNP129;DBSNP132;DP=14;HAPMAP;OMNI;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.220C>A;refseq.codingCoordStr_2=c.220C>A;refseq.codingCoordStr_3=c.220C>C;refseq.codingCoordStr_4=c.220C>C;refseq.codingCoordStr_5=c.220C>G;refseq.codingCoordStr_6=c.220C>G;refseq.codingCoordStr_7=c.220C>T;refseq.codingCoordStr_8=c.220C>T;refseq.codonCoord_1=74;refseq.codonCoord_2=74;refseq.codonCoord_3=74;refseq.codonCoord_4=74;refseq.codonCoord_5=74;refseq.codonCoord_6=74;refseq.codonCoord_7=74;refseq.codonCoord_8=74;refseq.end_1=10019169;refseq.end_2=10019169;refseq.end_3=10019169;refseq.end_4=10019169;refseq.end_5=10019169;refseq.end_6=10019169;refseq.end_7=10019169;refseq.end_8=10019169;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.haplotypeReference_5=C;refseq.haplotypeReference_6=C;refseq.haplotypeReference_7=C;refseq.haplotypeReference_8=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=613;refseq.mrnaCoord_2=549;refseq.mrnaCoord_3=613;refseq.mrnaCoord_4=549;refseq.mrnaCoord_5=613;refseq.mrnaCoord_6=549;refseq.mrnaCoord_7=613;refseq.mrnaCoord_8=549;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.P74T;refseq.proteinCoordStr_2=p.P74T;refseq.proteinCoordStr_3=p.P74P;refseq.proteinCoordStr_4=p.P74P;refseq.proteinCoordStr_5=p.P74A;refseq.proteinCoordStr_6=p.P74A;refseq.proteinCoordStr_7=p.P74S;refseq.proteinCoordStr_8=p.P74S;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceAA_4=Pro;refseq.referenceAA_5=Pro;refseq.referenceAA_6=Pro;refseq.referenceAA_7=Pro;refseq.referenceAA_8=Pro;refseq.referenceCodon_1=CCT;refseq.referenceCodon_2=CCT;refseq.referenceCodon_3=CCT;refseq.referenceCodon_4=CCT;refseq.referenceCodon_5=CCT;refseq.referenceCodon_6=CCT;refseq.referenceCodon_7=CCT;refseq.referenceCodon_8=CCT;refseq.spliceDist_1=-127;refseq.spliceDist_2=-127;refseq.spliceDist_3=-127;refseq.spliceDist_4=-127;refseq.spliceDist_5=-127;refseq.spliceDist_6=-127;refseq.spliceDist_7=-127;refseq.spliceDist_8=-127;refseq.start_1=10019169;refseq.start_2=10019169;refseq.start_3=10019169;refseq.start_4=10019169;refseq.start_5=10019169;refseq.start_6=10019169;refseq.start_7=10019169;refseq.start_8=10019169;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_
20 10032432 rs78089752 A . 367.04 PASS AC=0;AF=0.00;AN=6;DBSNP132;DP=18;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.1765A>A;refseq.codingCoordStr_2=c.1765A>A;refseq.codingCoordStr_3=c.1765A>C;refseq.codingCoordStr_4=c.1765A>C;refseq.codingCoordStr_5=c.1765A>G;refseq.codingCoordStr_6=c.1765A>G;refseq.codingCoordStr_7=c.1765A>T;refseq.codingCoordStr_8=c.1765A>T;refseq.codonCoord_1=589;refseq.codonCoord_2=589;refseq.codonCoord_3=589;refseq.codonCoord_4=589;refseq.codonCoord_5=589;refseq.codonCoord_6=589;refseq.codonCoord_7=589;refseq.codonCoord_8=589;refseq.end_1=10032432;refseq.end_2=10032432;refseq.end_3=10032432;refseq.end_4=10032432;refseq.end_5=10032432;refseq.end_6=10032432;refseq.end_7=10032432;refseq.end_8=10032432;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.haplotypeReference_5=A;refseq.haplotypeReference_6=A;refseq.haplotypeReference_7=A;refseq.haplotypeReference_8=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=2158;refseq.mrnaCoord_2=2094;refseq.mrnaCoord_3=2158;refseq.mrnaCoord_4=2094;refseq.mrnaCoord_5=2158;refseq.mrnaCoord_6=2094;refseq.mrnaCoord_7=2158;refseq.mrnaCoord_8=2094;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.I589I;refseq.proteinCoordStr_2=p.I589I;refseq.proteinCoordStr_3=p.I589L;refseq.proteinCoordStr_4=p.I589L;refseq.proteinCoordStr_5=p.I589V;refseq.proteinCoordStr_6=p.I589V;refseq.proteinCoordStr_7=p.I589F;refseq.proteinCoordStr_8=p.I589F;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceAA_3=Ile;refseq.referenceAA_4=Ile;refseq.referenceAA_5=Ile;refseq.referenceAA_6=Ile;refseq.referenceAA_7=Ile;refseq.referenceAA_8=Ile;refseq.referenceCodon_1=ATC;refseq.referenceCodon_2=ATC;refseq.referenceCodon_3=ATC;refseq.referenceCodon_4=ATC;refseq.referenceCodon_5=ATC;refseq.referenceCodon_6=ATC;refseq.referenceCodon_7=ATC;refseq.referenceCodon_8=ATC;refseq.spliceDist_1=-106;refseq.spliceDist_2=-106;refseq.spliceDist_3=-106;refseq.spliceDist_4=-106;refseq.spliceDist_5=-106;refseq.spliceDist_6=-106;refseq.spliceDist_7=-106;refseq.spliceDist_8=-106;refseq.start_1=10032432;refseq.start_2=10032432;refseq.start_3=10032432;refseq.start_4=10032432;refseq.start_5=10032432;refseq.start_6=10032432;refseq.start_7=10032432;refseq.start_8=10032432;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.t
20 10037119 . G . 469.85 PASS AC=0;AF=0.00;AN=4;DBSNP129;DP=3;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.*811G>A;refseq.codingCoordStr_2=c.*811G>A;refseq.codingCoordStr_3=c.*811G>C;refseq.codingCoordStr_4=c.*811G>C;refseq.codingCoordStr_5=c.*811G>G;refseq.codingCoordStr_6=c.*811G>G;refseq.codingCoordStr_7=c.*811G>T;refseq.codingCoordStr_8=c.*811G>T;refseq.end_1=10037119;refseq.end_2=10037119;refseq.end_3=10037119;refseq.end_4=10037119;refseq.end_5=10037119;refseq.end_6=10037119;refseq.end_7=10037119;refseq.end_8=10037119;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=3535;refseq.mrnaCoord_2=3471;refseq.mrnaCoord_3=3535;refseq.mrnaCoord_4=3471;refseq.mrnaCoord_5=3535;refseq.mrnaCoord_6=3471;refseq.mrnaCoord_7=3535;refseq.mrnaCoord_8=3471;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr3;refseq.positionType_2=utr3;refseq.positionType_3=utr3;refseq.positionType_4=utr3;refseq.positionType_5=utr3;refseq.positionType_6=utr3;refseq.positionType_7=utr3;refseq.positionType_8=utr3;refseq.spliceDist_1=-289;refseq.spliceDist_2=-289;refseq.spliceDist_3=-289;refseq.spliceDist_4=-289;refseq.spliceDist_5=-289;refseq.spliceDist_6=-289;refseq.spliceDist_7=-289;refseq.spliceDist_8=-289;refseq.start_1=10037119;refseq.start_2=10037119;refseq.start_3=10037119;refseq.start_4=10037119;refseq.start_5=10037119;refseq.start_6=10037119;refseq.start_7=10037119;refseq.start_8=10037119;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+ GT:DP:GQ:PL ./. 0/0:2:6:0,6,65 0/0:1:3:0,3,37
20 10047435 rs598275 G A 82495.04 PASS AC=6;AF=1.00;AN=6;DBSNP129;DBSNP132;DP=8;HAPMAP;OMNI GT:DP:GQ:PL 1/1:2:6:69,6,0 1/1:2:6:69,6,0 1/1:4:12:139,12,0