# Header from primary input:
##fileformat=VCFv4.0
##ApplyRecalibration="analysis_type=ApplyRecalibration input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[../combined.phase1.chr1.raw.snps.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false recal_file=projectConsensus.withHRun.chr1.tranches.recal tranches_file=projectConsensus.withHRun.tranches out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub ts_filter_level=99.87 ignore_filter=null mode=SNP"
##CombineVariants="analysis_type=CombineVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[1:123000001-126000000] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/1kg/processing/production_wgs_phase1/consensus/calls/chr1/AFR/AFR.phase1.chr1.42.raw.snps.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus/calls/chr1/ASN/ASN.phase1.chr1.42.raw.snps.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus/calls/chr1/AMR/AMR.phase1.chr1.42.raw.snps.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus/calls/chr1/EUR/EUR.phase1.chr1.42.raw.snps.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus/calls/chr1/AFR.admix/AFR.admix.phase1.chr1.42.raw.snps.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus/calls/chr1/ASN.admix/ASN.admix.phase1.chr1.42.raw.snps.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus/calls/chr1/AMR.admix/AMR.admix.phase1.chr1.42.raw.snps.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus/calls/chr1/EUR.admix/EUR.admix.phase1.chr1.42.raw.snps.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null quiet_output_mode=false debug_mode=false help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub genotypemergeoption=PRIORITIZE variantmergeoption=UNION rod_priority_list=AFR.admix,AMR.admix,EUR.admix,ASN.admix,AFR,AMR,EUR,ASN printComplexMerges=false filteredAreUncalled=false minimalVCF=false setKey=set assumeIdenticalSamples=false mergeInfoWithMaxAC=true"
##FILTER=<ID=TruthSensitivityTranche99.87to99.89,Description="Truth sensitivity tranche level at VSQ Lod: -1.5186 <= x < -1.0186">
##FILTER=<ID=TruthSensitivityTranche99.89to99.90,Description="Truth sensitivity tranche level at VSQ Lod: -1.8238 <= x < -1.5186">
##FILTER=<ID=TruthSensitivityTranche99.90to100.00+,Description="Truth sensitivity tranche level at VQS Lod < -16969.2078">
##FILTER=<ID=TruthSensitivityTranche99.90to100.00,Description="Truth sensitivity tranche level at VSQ Lod: -16969.2078 <= x < -1.8238">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##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=BaseQRankSum,Number=1,Type=Float,Description="Phred-scaled p-value From Wilcoxon Rank Sum Test of Alt Vs. Ref base qualities">
##INFO=<ID=BaseQRankSumZ,Number=1,Type=Float,Description="Z-score From Wilcoxon Rank Sum Test of Alt Vs. Ref base qualities">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Phred-scaled p-value From Wilcoxon Rank Sum Test of Alt Vs. Ref read mapping qualities">
##INFO=<ID=MQRankSumZ,Number=1,Type=Float,Description="Z-score From Wilcoxon Rank Sum Test of Alt Vs. Ref read mapping qualities">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Phred-scaled p-value From Wilcoxon Rank Sum Test of Alt Vs. Ref read position bias">
##INFO=<ID=ReadPosRankSumZ,Number=1,Type=Float,Description="Z-score From Wilcoxon Rank Sum Test of Alt Vs. Ref read position bias">
##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
##INFO=<ID=VQSLOD,Number=1,Type=Float,Description="log10-scaled probability of variant being true under the trained gaussian mixture model">
##INFO=<ID=set,Number=1,Type=String,Description="Source VCF for the merged record in CombineVariants">
##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/humgen/1kg/scratch/calls/chr1/CHB.phase1.chr1.42.cleaned.bam, /humgen/1kg/scratch/calls/chr1/CHS.phase1.chr1.42.cleaned.bam, /humgen/1kg/scratch/calls/chr1/CLM.phase1.chr1.42.cleaned.bam, /humgen/1kg/scratch/calls/chr1/JPT.phase1.chr1.42.cleaned.bam, /humgen/1kg/scratch/calls/chr1/MXL.phase1.chr1.42.cleaned.bam, /humgen/1kg/scratch/calls/chr1/PUR.phase1.chr1.42.cleaned.bam] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[1:123000001-126000000] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/1kg/processing/production_wgs_phase1/consensus/ALL.phase1.wgs.unionBC1.pass.sites.vcf, /humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=50 baq=CALCULATE_AS_NECESSARY baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null quiet_output_mode=false debug_mode=false help=false genotype_likelihoods_model=SNP p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=GENOTYPE_GIVEN_ALLELES output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=4.0 standard_min_confidence_threshold_for_emitting=4.0 noSLOD=false assume_single_sample_reads=null abort_at_too_much_coverage=-1 min_base_quality_score=17 min_mapping_quality_score=20 max_deletion_fraction=0.05 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 doContextDependentGapPenalties=true indelDebug=false dovit=false exactCalculation=LINEAR_EXPERIMENTAL output_all_callable_bases=false genotype=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[]"
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	
#http://genome.ucsc.edu/goldenPath/help/examples/vcfExampleTwo.vcf.chrom	http://genome.ucsc.edu/goldenPath/help/examples/vcfExampleTwo.vcf.pos	http://genome.ucsc.edu/goldenPath/help/examples/vcfExampleTwo.vcf.id	http://genome.ucsc.edu/goldenPath/help/examples/vcfExampleTwo.vcf.ref	http://genome.ucsc.edu/goldenPath/help/examples/vcfExampleTwo.vcf.alt	http://genome.ucsc.edu/goldenPath/help/examples/vcfExampleTwo.vcf.qual	http://genome.ucsc.edu/goldenPath/help/examples/vcfExampleTwo.vcf.filter	http://genome.ucsc.edu/goldenPath/help/examples/vcfExampleTwo.vcf.info	http://genome.ucsc.edu/goldenPath/help/examples/vcfExampleTwo.vcf.format	http://genome.ucsc.edu/goldenPath/help/examples/vcfExampleTwo.vcf.genotypes
21	33031822	rs17883296	G	T	89.31	PASS	AC=4;AF=0.0090;AN=446;BaseQRankSum=13.246;BaseQRankSumZ=-1.671;DB;DP=729;Dels=0.00;HRun=0;HaplotypeScore=0.3330;MQ=73.45;MQ0=0;MQRankSum=0.340;MQRankSumZ=1.437;QD=3.64;ReadPosRankSum=3.384;ReadPosRankSumZ=-0.103;SB=12.32;VQSLOD=6.3319;set=ALL12		
21	33031927	rs17878855	G	C	49.90	PASS	AC=6;AF=0.0167;AN=360;BaseQRankSum=17.394;BaseQRankSumZ=-2.092;DB;DP=719;Dels=0.00;HRun=0;HaplotypeScore=0.2819;MQ=69.68;MQ0=0;MQRankSum=0.068;MQRankSumZ=2.155;QD=2.84;ReadPosRankSum=0.781;ReadPosRankSumZ=0.975;SB=-68.62;VQSLOD=4.8372;set=ALL12		
21	33031974	rs7277748	A	G	1112.77	PASS	AC=44;AF=0.0902;AN=488;BaseQRankSum=7.100;BaseQRankSumZ=-0.860;DB;DP=808;Dels=0.00;HRun=0;HaplotypeScore=0.2530;MQ=102.07;MQ0=0;MQRankSum=0.043;MQRankSumZ=2.333;QD=13.04;ReadPosRankSum=5.771;ReadPosRankSumZ=-0.629;SB=-550.84;VQSLOD=7.9658;set=ALL12		
21	33031993	rs17881581	G	A	4.74	PASS	AC=1;AF=0.0028;AN=362;BaseQRankSum=0.097;BaseQRankSumZ=2.014;DB;DP=637;Dels=0.00;HRun=0;HaplotypeScore=0.2745;MQ=113.46;MQ0=0;MQRankSum=3.103;MQRankSumZ=-0.026;QD=1.19;ReadPosRankSum=8.697;ReadPosRankSumZ=-1.103;SB=-26.74;VQSLOD=0.0203;set=ALL12		
21	33031996	.	G	C	63.41	PASS	AC=1;AF=0.0013;AN=774;BaseQRankSum=1.660;BaseQRankSumZ=0.474;DP=1649;Dels=0.00;HRun=0;HaplotypeScore=0.2752;MQ=107.00;MQ0=0;MQRankSum=0.777;MQRankSumZ=0.979;QD=8.83;ReadPosRankSum=2.230;ReadPosRankSumZ=0.249;SB=-27.49;VQSLOD=6.8462;set=ALL12		
21	33032035	.	T	A	37.35	PASS	AC=3;AF=0.0063;AN=480;BaseQRankSum=11.243;BaseQRankSumZ=-1.439;DP=942;Dels=0.00;HRun=0;HaplotypeScore=0.2444;MQ=127.46;MQ0=0;MQRankSum=0.009;MQRankSumZ=2.876;QD=2.43;ReadPosRankSum=0.335;ReadPosRankSumZ=1.445;SB=-82.41;VQSLOD=3.0802;set=ALL12		
21	33032287	rs17881180	C	T	693.19	PASS	AC=33;AF=0.1078;AN=306;BaseQRankSum=0.000;BaseQRankSumZ=6.344;DB;DP=592;Dels=0.00;HRun=0;HaplotypeScore=0.3180;MQ=56.28;MQ0=0;MQRankSum=0.083;MQRankSumZ=2.077;QD=10.50;ReadPosRankSum=1.772;ReadPosRankSumZ=0.426;SB=-193.02;VQSLOD=7.5740;set=ALL12		
21	33032513	.	T	G	314.20	TruthSensitivityTranche99.90to100.00	AC=31;AF=0.0503;AN=616;BaseQRankSum=200.000;BaseQRankSumZ=-11.808;DP=878;Dels=0.00;HRun=1;HaplotypeScore=0.3664;MQ=79.36;MQ0=0;MQRankSum=35.720;MQRankSumZ=-3.462;QD=2.68;ReadPosRankSum=56.828;ReadPosRankSumZ=-4.604;SB=102.83;VQSLOD=-2.6107;set=ALL12		
21	33032617	.	C	T	54.34	PASS	AC=6;AF=0.0091;AN=660;BaseQRankSum=7.642;BaseQRankSumZ=-0.946;DP=877;Dels=0.00;HRun=0;HaplotypeScore=0.2102;MQ=80.34;MQ0=0;MQRankSum=0.036;MQRankSumZ=2.399;QD=2.78;ReadPosRankSum=3.958;ReadPosRankSumZ=-0.248;SB=-59.21;VQSLOD=3.4615;set=ALL12		
21	33032857	rs114905802	C	T	245.12	PASS	AC=9;AF=0.0130;AN=692;BaseQRankSum=21.368;BaseQRankSumZ=-2.442;DB;DP=1821;Dels=0.00;HRun=1;HaplotypeScore=0.2056;MQ=107.08;MQ0=0;MQRankSum=1.162;MQRankSumZ=0.723;QD=5.56;ReadPosRankSum=39.605;ReadPosRankSumZ=-3.696;SB=-190.88;VQSLOD=2.5953;set=ALL12		
21	33032895	.	C	G	152.26	PASS	AC=6;AF=0.0083;AN=720;BaseQRankSum=58.356;BaseQRankSumZ=-4.676;DP=1565;Dels=0.00;HRun=0;HaplotypeScore=0.3012;MQ=114.91;MQ0=0;MQRankSum=0.046;MQRankSumZ=2.304;QD=4.23;ReadPosRankSum=1.319;ReadPosRankSumZ=0.637;SB=-131.21;VQSLOD=6.4241;set=ALL12		
21	33032896	rs17884260	T	G	66.67	PASS	AC=3;AF=0.0043;AN=692;BaseQRankSum=84.817;BaseQRankSumZ=-5.801;DB;DP=1977;Dels=0.00;HRun=0;HaplotypeScore=0.2693;MQ=105.15;MQ0=0;MQRankSum=0.171;MQRankSumZ=1.766;QD=2.92;ReadPosRankSum=11.094;ReadPosRankSumZ=-1.421;SB=-80.22;VQSLOD=4.9551;set=ALL12		
21	33032988	rs6650814	C	A	11985.86	PASS	AC=129;AF=0.1822;AN=708;BaseQRankSum=0.000;BaseQRankSumZ=14.714;DB;DP=2268;Dels=0.00;HRun=0;HaplotypeScore=0.2612;MQ=113.25;MQ0=0;MQRankSum=5.830;MQRankSumZ=-0.640;QD=17.00;ReadPosRankSum=23.720;ReadPosRankSumZ=-2.632;SB=-4896.73;VQSLOD=7.5766;set=ALL12		
21	33033001	rs4816405	C	G	30051.70	PASS	AC=352;AF=0.3877;AN=908;BaseQRankSum=94.306;BaseQRankSumZ=-6.157;DB;DP=2745;Dels=0.00;HRun=0;HaplotypeScore=0.2333;MQ=114.14;MQ0=0;MQRankSum=0.747;MQRankSumZ=1.003;QD=20.35;ReadPosRankSum=14.877;ReadPosRankSumZ=-1.845;SB=-13678.18;VQSLOD=8.5130;set=ALL12		
21	33033026	.	G	A	46.46	PASS	AC=2;AF=0.0041;AN=482;BaseQRankSum=0.615;BaseQRankSumZ=1.117;DP=1670;Dels=0.00;HRun=1;HaplotypeScore=0.2867;MQ=117.60;MQ0=0;MQRankSum=0.092;MQRankSumZ=2.033;QD=4.65;ReadPosRankSum=0.422;ReadPosRankSumZ=1.325;SB=-30.11;VQSLOD=5.4623;set=ALL12		
21	33033070	rs17884040	A	G	35.62	PASS	AC=3;AF=0.0054;AN=558;BaseQRankSum=38.206;BaseQRankSumZ=-3.613;DB;DP=1565;Dels=0.00;HRun=0;HaplotypeScore=0.2539;MQ=104.49;MQ0=0;MQRankSum=1.084;MQRankSumZ=0.769;QD=5.09;ReadPosRankSum=3.969;ReadPosRankSumZ=-0.251;SB=-37.23;VQSLOD=5.9914;set=ALL12		
21	33033082	rs17880795	G	C	151.24	PASS	AC=2;AF=0.0028;AN=708;BaseQRankSum=5.461;BaseQRankSumZ=-0.570;DB;DP=2318;Dels=0.00;HRun=0;HaplotypeScore=0.2582;MQ=113.37;MQ0=0;MQRankSum=0.223;MQRankSumZ=1.645;QD=9.86;ReadPosRankSum=1.282;ReadPosRankSumZ=0.657;SB=-48.97;VQSLOD=8.4712;set=ALL12		
21	33033399	.	A	G	12.52	PASS	AC=1;AF=0.00093;AN=1070;BaseQRankSum=6.024;BaseQRankSumZ=-0.675;DP=2565;Dels=0.00;HRun=0;HaplotypeScore=0.1925;MQ=114.35;MQ0=0;MQRankSum=2.666;MQRankSumZ=0.104;QD=5.42;ReadPosRankSum=4.384;ReadPosRankSumZ=-0.347;SB=-31.19;VQSLOD=3.1579;set=ALL12		
21	33033650	.	T	A	9.35	PASS	AC=1;AF=0.0014;AN=700;BaseQRankSum=4.637;BaseQRankSumZ=-0.402;DP=1821;Dels=0.00;HRun=0;HaplotypeScore=0.1992;MQ=97.23;MQ0=0;MQRankSum=1.747;MQRankSumZ=0.437;QD=3.43;ReadPosRankSum=8.408;ReadPosRankSumZ=-1.061;SB=1.39;VQSLOD=2.1944;set=ALL12		
21	33033723	rs17885219	C	T	964.07	PASS	AC=36;AF=0.0465;AN=774;BaseQRankSum=2.002;BaseQRankSumZ=0.334;DB;DP=1555;Dels=0.00;HRun=1;HaplotypeScore=0.1820;MQ=51.03;MQ0=94;MQRankSum=1.428;MQRankSumZ=0.582;QD=9.10;ReadPosRankSum=3.992;ReadPosRankSumZ=-0.256;SB=-594.88;VQSLOD=6.4602;set=ALL12		
21	33033828	rs17882967	C	T	109.77	PASS	AC=7;AF=0.0098;AN=712;BaseQRankSum=0.783;BaseQRankSumZ=0.974;DB;DP=1807;Dels=0.00;HRun=0;HaplotypeScore=0.2930;MQ=60.85;MQ0=106;MQRankSum=0.312;MQRankSumZ=1.482;QD=3.23;ReadPosRankSum=7.150;ReadPosRankSumZ=-0.868;SB=-73.91;VQSLOD=5.6132;set=ALL12		
21	33033873	.	C	G	51.55	PASS	AC=1;AF=0.0013;AN=798;BaseQRankSum=12.578;BaseQRankSumZ=-1.596;DP=1746;Dels=0.00;HRun=0;HaplotypeScore=0.2755;MQ=55.55;MQ0=54;MQRankSum=16.720;MQRankSumZ=-2.028;QD=6.16;ReadPosRankSum=6.025;ReadPosRankSumZ=-0.675;SB=-23.89;VQSLOD=3.6353;set=ALL12		
21	33034023	.	A	G	5.50	PASS	AC=1;AF=0.00094;AN=1060;BaseQRankSum=12.685;BaseQRankSumZ=-1.608;DP=2402;Dels=0.00;HRun=0;HaplotypeScore=0.1906;MQ=101.23;MQ0=0;MQRankSum=1.088;MQRankSumZ=0.767;QD=1.09;ReadPosRankSum=0.644;ReadPosRankSumZ=1.090;SB=1.91;VQSLOD=1.6689;set=ALL12		
21	33034082	rs17883270	C	G	510.75	PASS	AC=15;AF=0.0214;AN=700;BaseQRankSum=121.420;BaseQRankSumZ=-7.080;DB;DP=1872;Dels=0.00;HRun=0;HaplotypeScore=0.2138;MQ=111.93;MQ0=0;MQRankSum=0.000;MQRankSumZ=4.477;QD=8.28;ReadPosRankSum=3.273;ReadPosRankSumZ=-0.074;SB=-252.26;VQSLOD=7.2215;set=ALL12		
21	33034103	rs17878802	C	G	1981.71	PASS	AC=38;AF=0.0549;AN=692;BaseQRankSum=0.000;BaseQRankSumZ=5.861;DB;DP=1811;Dels=0.00;HRun=1;HaplotypeScore=0.1842;MQ=111.66;MQ0=0;MQRankSum=0.000;MQRankSumZ=3.946;QD=10.83;ReadPosRankSum=13.487;ReadPosRankSumZ=-1.697;SB=-964.38;VQSLOD=6.5635;set=ALL12		
21	33034171	rs17881807	A	G	423.77	PASS	AC=8;AF=0.0112;AN=712;BaseQRankSum=28.491;BaseQRankSumZ=-2.986;DB;DP=2120;Dels=0.00;HRun=0;HaplotypeScore=0.2553;MQ=120.80;MQ0=0;MQRankSum=6.039;MQRankSumZ=-0.678;QD=8.39;ReadPosRankSum=3.403;ReadPosRankSumZ=-0.109;SB=-224.92;VQSLOD=7.3418;set=ALL12		
21	33034175	.	A	C	19.29	PASS	AC=1;AF=0.0014;AN=712;BaseQRankSum=15.853;BaseQRankSumZ=-1.943;DP=2120;Dels=0.00;HRun=1;HaplotypeScore=0.2443;MQ=120.34;MQ0=0;MQRankSum=0.447;MQRankSumZ=1.294;QD=4.49;ReadPosRankSum=11.463;ReadPosRankSumZ=-1.465;SB=-28.26;VQSLOD=3.4909;set=ALL12		
21	33034245	.	A	C	107.13	PASS	AC=1;AF=0.0014;AN=702;BaseQRankSum=62.612;BaseQRankSumZ=-4.874;DP=2205;Dels=0.00;HRun=0;HaplotypeScore=0.3273;MQ=123.13;MQ0=1;MQRankSum=0.768;MQRankSumZ=0.986;QD=6.20;ReadPosRankSum=10.449;ReadPosRankSumZ=-1.340;SB=-71.81;VQSLOD=6.9430;set=ALL12		
21	33034279	.	C	A	63.14	PASS	AC=1;AF=0.00091;AN=1098;BaseQRankSum=26.348;BaseQRankSumZ=-2.831;DP=3012;Dels=0.00;HRun=0;HaplotypeScore=0.1693;MQ=125.29;MQ0=0;MQRankSum=6.970;MQRankSumZ=-0.838;QD=10.21;ReadPosRankSum=9.153;ReadPosRankSumZ=-1.167;SB=-56.06;VQSLOD=6.2303;set=ALL12		
21	33034370	.	A	G	119.43	PASS	AC=1;AF=0.0014;AN=702;BaseQRankSum=0.023;BaseQRankSumZ=2.564;DP=2076;Dels=0.00;HRun=0;HaplotypeScore=0.2506;MQ=105.55;MQ0=0;MQRankSum=0.335;MQRankSumZ=1.445;QD=16.72;ReadPosRankSum=3.187;ReadPosRankSumZ=-0.050;SB=-32.94;VQSLOD=8.0134;set=ALL12		
21	33034385	.	C	G	5.36	TruthSensitivityTranche99.87to99.89	AC=1;AF=0.0014;AN=704;BaseQRankSum=3.352;BaseQRankSumZ=-0.095;DP=2034;Dels=0.00;HRun=0;HaplotypeScore=0.2713;MQ=102.85;MQ0=0;MQRankSum=0.448;MQRankSumZ=1.293;QD=0.71;ReadPosRankSum=11.236;ReadPosRankSumZ=-1.438;SB=7.49;VQSLOD=-1.3958;set=ALL12		
21	33034448	.	C	T	183.22	PASS	AC=2;AF=0.00186;AN=1078;BaseQRankSum=5.256;BaseQRankSumZ=-0.530;DP=2788;Dels=0.00;HRun=1;HaplotypeScore=0.1393;MQ=117.48;MQ0=1;MQRankSum=2.806;MQRankSumZ=0.061;QD=10.69;ReadPosRankSum=2.212;ReadPosRankSumZ=0.256;SB=-87.15;VQSLOD=6.1021;set=ALL12		
21	33034657	.	A	G	111.92	PASS	AC=2;AF=0.0028;AN=714;BaseQRankSum=22.135;BaseQRankSumZ=-2.505;DP=2617;Dels=0.00;HRun=1;HaplotypeScore=0.2099;MQ=116.17;MQ0=0;MQRankSum=0.658;MQRankSumZ=1.078;QD=8.35;ReadPosRankSum=5.347;ReadPosRankSumZ=-0.548;SB=-69.52;VQSLOD=6.6810;set=ALL12		
21	33034731	.	A	C	59.35	PASS	AC=1;AF=0.0011;AN=924;BaseQRankSum=20.757;BaseQRankSumZ=-2.391;DP=2790;Dels=0.00;HRun=1;HaplotypeScore=0.2924;MQ=108.90;MQ0=0;MQRankSum=9.480;MQRankSumZ=-1.212;QD=6.35;ReadPosRankSum=4.760;ReadPosRankSumZ=-0.428;SB=-24.41;VQSLOD=4.2188;set=ALL12		
21	33034749	.	G	A	77.73	PASS	AC=1;AF=0.0014;AN=714;BaseQRankSum=5.893;BaseQRankSumZ=-0.651;DP=2337;Dels=0.00;HRun=2;HaplotypeScore=0.3410;MQ=107.74;MQ0=0;MQRankSum=0.571;MQRankSumZ=1.160;QD=12.63;ReadPosRankSum=3.075;ReadPosRankSumZ=-0.018;SB=-24.39;VQSLOD=5.0184;set=ALL12		
21	33034791	.	G	T	144.79	PASS	AC=5;AF=0.0070;AN=710;BaseQRankSum=20.629;BaseQRankSumZ=-2.380;DP=2263;Dels=0.00;HRun=3;HaplotypeScore=0.4875;MQ=123.03;MQ0=0;MQRankSum=27.688;MQRankSumZ=-2.928;QD=4.01;ReadPosRankSum=15.220;ReadPosRankSumZ=-1.880;SB=-113.41;VQSLOD=1.1316;set=ALL12		
21	33034892	rs4998557	G	A	27796.17	PASS	AC=354;AF=0.3933;AN=900;BaseQRankSum=29.273;BaseQRankSumZ=-3.040;DB;DP=2604;Dels=0.00;HRun=0;HaplotypeScore=0.2250;MQ=114.54;MQ0=0;MQRankSum=4.258;MQRankSumZ=-0.318;QD=19.25;ReadPosRankSum=12.090;ReadPosRankSumZ=-1.540;SB=-11515.51;VQSLOD=8.8298;set=ALL12		
21	33035007	.	T	C	13.55	PASS	AC=2;AF=0.0028;AN=704;BaseQRankSum=3.645;BaseQRankSumZ=-0.171;DP=1987;Dels=0.00;HRun=0;HaplotypeScore=0.2736;MQ=99.96;MQ0=0;MQRankSum=0.102;MQRankSumZ=1.991;QD=2.17;ReadPosRankSum=3.255;ReadPosRankSumZ=-0.069;SB=13.54;VQSLOD=2.2349;set=ALL12		
21	33035107	.	C	T	48.93	PASS	AC=3;AF=0.0044;AN=686;BaseQRankSum=2.234;BaseQRankSumZ=0.248;DP=1585;Dels=0.00;HRun=1;HaplotypeScore=0.2635;MQ=50.18;MQ0=81;MQRankSum=5.716;MQRankSumZ=-0.618;QD=3.27;ReadPosRankSum=2.505;ReadPosRankSumZ=0.155;SB=-17.77;VQSLOD=2.3998;set=ALL12		
21	33035185	.	G	A	72.07	PASS	AC=6;AF=0.0069;AN=874;BaseQRankSum=0.002;BaseQRankSumZ=3.305;DP=1817;Dels=0.00;HRun=0;HaplotypeScore=0.1904;MQ=54.55;MQ0=177;MQRankSum=15.362;MQRankSumZ=-1.894;QD=1.99;ReadPosRankSum=2.962;ReadPosRankSumZ=0.014;SB=-4.63;VQSLOD=-0.0995;set=ALL12		
21	33035381	.	G	C	10.45	PASS	AC=3;AF=0.0034;AN=882;BaseQRankSum=13.644;BaseQRankSumZ=-1.715;DP=2189;Dels=0.00;HRun=0;HaplotypeScore=0.3119;MQ=99.94;MQ0=0;MQRankSum=11.520;MQRankSumZ=-1.472;QD=0.51;ReadPosRankSum=1.131;ReadPosRankSumZ=0.742;SB=-31.98;VQSLOD=-0.8146;set=ALL12		
21	33035601	.	T	C	125.12	TruthSensitivityTranche99.90to100.00	AC=13;AF=0.0187;AN=694;BaseQRankSum=69.208;BaseQRankSumZ=-5.165;DP=1554;Dels=0.00;HRun=1;HaplotypeScore=0.2263;MQ=45.97;MQ0=107;MQRankSum=35.222;MQRankSumZ=-3.431;QD=0.92;ReadPosRankSum=27.271;ReadPosRankSumZ=-2.899;SB=32.34;VQSLOD=-2.0383;set=ALL12		
21	33035611	.	C	T	114.62	TruthSensitivityTranche99.90to100.00	AC=19;AF=0.0217;AN=874;BaseQRankSum=1.548;BaseQRankSumZ=0.525;DP=1918;Dels=0.00;HRun=0;HaplotypeScore=0.2539;MQ=52.00;MQ0=119;MQRankSum=36.885;MQRankSumZ=-3.534;QD=0.52;ReadPosRankSum=8.239;ReadPosRankSumZ=-1.036;SB=46.06;VQSLOD=-3.2277;set=ALL12		
21	33035656	rs116260263	A	G	117.13	PASS	AC=2;AF=0.0030;AN=672;BaseQRankSum=53.210;BaseQRankSumZ=-4.427;DB;DP=1941;Dels=0.00;HRun=0;HaplotypeScore=0.2976;MQ=56.79;MQ0=28;MQRankSum=7.150;MQRankSumZ=-0.868;QD=6.10;ReadPosRankSum=13.000;ReadPosRankSumZ=-1.644;SB=-109.98;VQSLOD=4.6427;set=ALL12		
21	33035730	.	A	G	173.12	PASS	AC=1;AF=0.0015;AN=650;BaseQRankSum=5.845;BaseQRankSumZ=-0.642;DP=2189;Dels=0.00;HRun=0;HaplotypeScore=0.3206;MQ=66.89;MQ0=1;MQRankSum=0.133;MQRankSumZ=1.878;QD=15.49;ReadPosRankSum=1.270;ReadPosRankSumZ=0.663;SB=-28.95;VQSLOD=7.3998;set=ALL12		
21	33035740	.	T	G	27.70	PASS	AC=1;AF=0.00094;AN=1068;BaseQRankSum=8.307;BaseQRankSumZ=-1.046;DP=2796;Dels=0.00;HRun=0;HaplotypeScore=0.1942;MQ=79.54;MQ0=1;MQRankSum=0.876;MQRankSumZ=0.905;QD=4.32;ReadPosRankSum=8.762;ReadPosRankSumZ=-1.112;SB=9.68;VQSLOD=4.4588;set=ALL12		
21	33035963	rs17884233	G	C	2211.92	PASS	AC=40;AF=0.0585;AN=684;BaseQRankSum=34.100;BaseQRankSumZ=-3.360;DB;DP=2072;Dels=0.00;HRun=0;HaplotypeScore=0.3000;MQ=101.50;MQ0=0;MQRankSum=0.000;MQRankSumZ=5.133;QD=8.94;ReadPosRankSum=0.249;ReadPosRankSumZ=1.591;SB=-1091.94;VQSLOD=7.4181;set=ALL12		
21	33035995	rs16988404	T	A	1978.35	PASS	AC=41;AF=0.03761;AN=1090;BaseQRankSum=52.379;BaseQRankSumZ=-4.386;DB;DP=2750;Dels=0.00;HRun=0;HaplotypeScore=0.2386;MQ=113.60;MQ0=0;MQRankSum=2.960;MQRankSumZ=0.015;QD=9.70;ReadPosRankSum=0.775;ReadPosRankSumZ=0.980;SB=-1414.33;VQSLOD=7.7157;set=ALL12		
21	33036391	rs10432782	T	G	19342.56	PASS	AC=344;AF=0.3891;AN=884;BaseQRankSum=200.000;BaseQRankSumZ=-14.099;DB;DP=2032;Dels=0.00;HRun=0;HaplotypeScore=0.2090;MQ=62.01;MQ0=2;MQRankSum=4.820;MQRankSumZ=-0.441;QD=18.20;ReadPosRankSum=14.692;ReadPosRankSumZ=-1.826;SB=-10011.10;VQSLOD=8.0674;set=ALL12		
21	33036441	.	C	T	52.16	PASS	AC=2;AF=0.0030;AN=656;BaseQRankSum=0.002;BaseQRankSumZ=3.309;DP=1788;Dels=0.00;HRun=0;HaplotypeScore=0.2993;MQ=55.09;MQ0=40;MQRankSum=0.088;MQRankSumZ=2.051;QD=6.65;ReadPosRankSum=15.433;ReadPosRankSumZ=-1.901;SB=-31.76;VQSLOD=6.1505;set=ALL12		
21	33036476	.	G	T	396.98	PASS	AC=12;AF=0.0176;AN=680;BaseQRankSum=12.837;BaseQRankSumZ=-1.625;DP=1828;Dels=0.00;HRun=0;HaplotypeScore=0.2206;MQ=54.67;MQ0=28;MQRankSum=0.000;MQRankSumZ=4.468;QD=7.73;ReadPosRankSum=9.846;ReadPosRankSumZ=-1.261;SB=-228.61;VQSLOD=6.5777;set=ALL12		
21	33036493	.	C	T	400.07	PASS	AC=12;AF=0.0177;AN=678;BaseQRankSum=0.008;BaseQRankSumZ=2.901;DP=1885;Dels=0.00;HRun=0;HaplotypeScore=0.2591;MQ=54.99;MQ0=47;MQRankSum=0.087;MQRankSumZ=2.057;QD=7.84;ReadPosRankSum=0.626;ReadPosRankSumZ=1.107;SB=-174.40;VQSLOD=7.4470;set=ALL12		
21	33036529	.	A	G	64.65	PASS	AC=2;AF=0.0029;AN=688;BaseQRankSum=48.230;BaseQRankSumZ=-4.173;DP=2021;Dels=0.00;HRun=0;HaplotypeScore=0.3241;MQ=56.87;MQ0=7;MQRankSum=2.881;MQRankSumZ=0.038;QD=3.08;ReadPosRankSum=0.300;ReadPosRankSumZ=1.500;SB=-80.80;VQSLOD=4.8415;set=ALL12		
21	33036561	.	C	G	59.41	PASS	AC=1;AF=0.0014;AN=698;BaseQRankSum=6.203;BaseQRankSumZ=-0.707;DP=2200;Dels=0.00;HRun=0;HaplotypeScore=0.2135;MQ=62.41;MQ0=47;MQRankSum=0.192;MQRankSumZ=1.714;QD=6.41;ReadPosRankSum=1.866;ReadPosRankSumZ=0.387;SB=-48.83;VQSLOD=7.2195;set=ALL12		
21	33036899	rs17880490	G	A	726.68	PASS	AC=10;AF=0.0144;AN=694;BaseQRankSum=0.034;BaseQRankSumZ=2.413;DB;DP=2277;Dels=0.00;HRun=0;HaplotypeScore=0.1974;MQ=114.21;MQ0=0;MQRankSum=0.186;MQRankSumZ=1.728;QD=8.86;ReadPosRankSum=3.855;ReadPosRankSumZ=-0.223;SB=-420.50;VQSLOD=8.1919;set=ALL12		
21	33036950	.	G	C	12.36	PASS	AC=1;AF=0.0011;AN=876;BaseQRankSum=1.709;BaseQRankSumZ=0.453;DP=2179;Dels=0.00;HRun=0;HaplotypeScore=0.2236;MQ=54.69;MQ0=59;MQRankSum=0.426;MQRankSumZ=1.320;QD=3.41;ReadPosRankSum=3.265;ReadPosRankSumZ=-0.071;SB=1.18;VQSLOD=2.7267;set=ALL12		
21	33036954	rs17886025	C	T	76.35	PASS	AC=2;AF=0.0030;AN=656;BaseQRankSum=0.014;BaseQRankSumZ=2.731;DB;DP=1771;Dels=0.00;HRun=0;HaplotypeScore=0.2310;MQ=54.34;MQ0=58;MQRankSum=2.981;MQRankSumZ=0.008;QD=6.49;ReadPosRankSum=5.138;ReadPosRankSumZ=-0.506;SB=-85.09;VQSLOD=7.8778;set=ALL12		
21	33037032	rs17883461	T	C	60.84	PASS	AC=2;AF=0.0041;AN=482;BaseQRankSum=25.628;BaseQRankSumZ=-2.778;DB;DP=1062;Dels=0.00;HRun=0;HaplotypeScore=0.1960;MQ=48.75;MQ0=99;MQRankSum=4.661;MQRankSumZ=-0.407;QD=4.80;ReadPosRankSum=1.846;ReadPosRankSumZ=0.395;SB=-16.86;VQSLOD=5.7872;set=ALL12		
21	33037089	.	G	A	19.12	PASS	AC=5;AF=0.0074;AN=676;BaseQRankSum=0.441;BaseQRankSumZ=1.301;DP=1837;Dels=0.00;HRun=0;HaplotypeScore=0.2809;MQ=47.10;MQ0=309;MQRankSum=0.735;MQRankSumZ=1.012;QD=1.06;ReadPosRankSum=0.831;ReadPosRankSumZ=0.938;SB=-34.41;VQSLOD=1.8682;set=ALL12		
21	33037143	.	A	G	153.58	TruthSensitivityTranche99.90to100.00	AC=22;AF=0.0225;AN=976;BaseQRankSum=23.893;BaseQRankSumZ=-2.645;DP=1972;Dels=0.00;HRun=1;HaplotypeScore=0.1877;MQ=60.92;MQ0=48;MQRankSum=200.000;MQRankSumZ=-9.110;QD=1.37;ReadPosRankSum=108.874;ReadPosRankSumZ=-6.668;SB=-118.87;VQSLOD=-5.0665;set=ALL12		
21	33037150	rs17886606	C	G	544.25	PASS	AC=16;AF=0.0241;AN=664;BaseQRankSum=17.977;BaseQRankSumZ=-2.146;DB;DP=1450;Dels=0.00;HRun=0;HaplotypeScore=0.3635;MQ=53.64;MQ0=17;MQRankSum=0.005;MQRankSumZ=3.030;QD=6.89;ReadPosRankSum=1.507;ReadPosRankSumZ=0.544;SB=-350.51;VQSLOD=7.1443;set=ALL12		
21	33037171	.	C	A	291.24	TruthSensitivityTranche99.90to100.00	AC=43;AF=0.0444;AN=968;BaseQRankSum=0.000;BaseQRankSumZ=4.659;DP=1845;Dels=0.00;HRun=0;HaplotypeScore=0.2265;MQ=61.48;MQ0=75;MQRankSum=200.000;MQRankSumZ=-10.078;QD=1.41;ReadPosRankSum=0.000;ReadPosRankSumZ=7.190;SB=-125.63;VQSLOD=-5.3865;set=ALL12		
21	33037175	.	T	A	293.23	TruthSensitivityTranche99.90to100.00	AC=40;AF=0.0416;AN=962;BaseQRankSum=8.789;BaseQRankSumZ=-1.116;DP=1876;Dels=0.00;HRun=0;HaplotypeScore=0.2252;MQ=61.88;MQ0=86;MQRankSum=200.000;MQRankSumZ=-10.655;QD=1.47;ReadPosRankSum=0.000;ReadPosRankSumZ=8.149;SB=-123.71;VQSLOD=-5.3895;set=ALL12		
21	33037177	.	T	C	341.43	TruthSensitivityTranche99.90to100.00	AC=46;AF=0.0486;AN=946;BaseQRankSum=22.674;BaseQRankSumZ=-2.549;DP=1871;Dels=0.00;HRun=1;HaplotypeScore=0.2479;MQ=62.04;MQ0=89;MQRankSum=200.000;MQRankSumZ=-10.596;QD=1.60;ReadPosRankSum=0.000;ReadPosRankSumZ=7.165;SB=-134.87;VQSLOD=-4.5666;set=ALL12		
21	33037346	rs76067554	C	G	375.49	PASS	AC=14;AF=0.0159;AN=880;BaseQRankSum=66.807;BaseQRankSumZ=-5.061;DB;DP=1995;Dels=0.00;HRun=4;HaplotypeScore=0.1907;MQ=106.51;MQ0=0;MQRankSum=2.292;MQRankSumZ=0.227;QD=5.83;ReadPosRankSum=6.788;ReadPosRankSumZ=-0.808;SB=-266.18;VQSLOD=4.3990;set=ALL12		
21	33037481	.	A	T	56.83	PASS	AC=2;AF=0.0026;AN=768;BaseQRankSum=2.478;BaseQRankSumZ=0.164;DP=1710;Dels=0.00;HRun=0;HaplotypeScore=0.1903;MQ=61.66;MQ0=1;MQRankSum=0.247;MQRankSumZ=1.596;QD=2.83;ReadPosRankSum=6.542;ReadPosRankSumZ=-0.766;SB=-156.56;VQSLOD=1.1146;set=ALL12		
21	33037482	rs9967983	A	T	26513.94	PASS	AC=516;AF=0.6898;AN=748;BaseQRankSum=50.364;BaseQRankSumZ=-4.284;DB;DP=1698;Dels=0.00;HRun=7;HaplotypeScore=0.1783;MQ=58.74;MQ0=1;MQRankSum=0.000;MQRankSumZ=6.835;QD=19.89;ReadPosRankSum=15.394;ReadPosRankSumZ=-1.898;SB=-17774.29;VQSLOD=1.4572;set=ALL12		
21	33037564	rs11567845	A	G	21213.74	PASS	AC=301;AF=0.29452;AN=1022;BaseQRankSum=200.000;BaseQRankSumZ=-11.076;DB;DP=2197;Dels=0.00;HRun=0;HaplotypeScore=0.2024;MQ=107.60;MQ0=0;MQRankSum=13.625;MQRankSumZ=-1.713;QD=18.77;ReadPosRankSum=1.046;ReadPosRankSumZ=0.792;SB=-8448.14;VQSLOD=7.8365;set=ALL12		
21	33037633	.	T	G	30.59	PASS	AC=1;AF=0.0011;AN=910;BaseQRankSum=25.487;BaseQRankSumZ=-2.767;DP=2522;Dels=0.00;HRun=1;HaplotypeScore=0.2013;MQ=119.14;MQ0=0;MQRankSum=0.168;MQRankSumZ=1.775;QD=5.66;ReadPosRankSum=10.034;ReadPosRankSumZ=-1.286;SB=1.04;VQSLOD=2.7599;set=ALL12		
21	33037638	rs78694163	A	G	406.46	PASS	AC=5;AF=0.0054;AN=918;BaseQRankSum=52.137;BaseQRankSumZ=-4.374;DB;DP=2558;Dels=0.00;HRun=0;HaplotypeScore=0.2238;MQ=115.51;MQ0=0;MQRankSum=8.640;MQRankSumZ=-1.095;QD=12.36;ReadPosRankSum=12.049;ReadPosRankSumZ=-1.535;SB=-268.86;VQSLOD=5.8758;set=ALL12		
21	33037786	.	G	A	140.90	PASS	AC=3;AF=0.0065;AN=464;BaseQRankSum=0.002;BaseQRankSumZ=3.331;DP=1273;Dels=0.00;HRun=0;HaplotypeScore=0.2379;MQ=126.47;MQ0=0;MQRankSum=1.428;MQRankSumZ=0.582;QD=5.72;ReadPosRankSum=0.046;ReadPosRankSumZ=2.306;SB=-17.98;VQSLOD=5.3210;set=ALL12		
21	33037870	rs17885303	C	T	391.66	PASS	AC=11;AF=0.01058;AN=1040;BaseQRankSum=0.000;BaseQRankSumZ=3.979;DB;DP=2521;Dels=0.00;HRun=0;HaplotypeScore=0.2700;MQ=99.96;MQ0=0;MQRankSum=0.074;MQRankSumZ=2.123;QD=6.68;ReadPosRankSum=4.020;ReadPosRankSumZ=-0.263;SB=-330.52;VQSLOD=8.4928;set=ALL12		
21	33037876	.	T	C	54.24	PASS	AC=1;AF=0.0022;AN=452;BaseQRankSum=27.538;BaseQRankSumZ=-2.918;DP=1124;Dels=0.00;HRun=1;HaplotypeScore=0.1646;MQ=104.75;MQ0=0;MQRankSum=0.651;MQRankSumZ=1.084;QD=4.82;ReadPosRankSum=1.775;ReadPosRankSumZ=0.425;SB=7.21;VQSLOD=4.8793;set=ALL12		
21	33037958	rs118132937	C	T	311.19	PASS	AC=11;AF=0.01034;AN=1064;BaseQRankSum=0.000;BaseQRankSumZ=4.132;DB;DP=2794;Dels=0.00;HRun=0;HaplotypeScore=0.2162;MQ=101.11;MQ0=0;MQRankSum=0.002;MQRankSumZ=3.336;QD=7.07;ReadPosRankSum=0.616;ReadPosRankSumZ=1.116;SB=-213.50;VQSLOD=7.0702;set=ALL12		
21	33038065	.	A	G	21.70	PASS	AC=2;AF=0.0028;AN=704;BaseQRankSum=3.170;BaseQRankSumZ=-0.045;DP=2154;Dels=0.00;HRun=0;HaplotypeScore=0.2690;MQ=115.12;MQ0=0;MQRankSum=0.642;MQRankSumZ=1.092;QD=2.35;ReadPosRankSum=4.438;ReadPosRankSumZ=-0.359;SB=-32.29;VQSLOD=0.8871;set=ALL12		
21	33038142	.	T	C	57.54	PASS	AC=1;AF=0.0011;AN=916;BaseQRankSum=32.147;BaseQRankSumZ=-3.234;DP=2744;Dels=0.00;HRun=0;HaplotypeScore=0.2475;MQ=128.29;MQ0=0;MQRankSum=10.108;MQRankSumZ=-1.296;QD=4.61;ReadPosRankSum=12.893;ReadPosRankSumZ=-1.632;SB=-48.81;VQSLOD=5.4255;set=ALL12		
21	33038188	.	A	G	77.98	PASS	AC=3;AF=0.0041;AN=730;BaseQRankSum=26.754;BaseQRankSumZ=-2.861;DP=1535;Dels=0.00;HRun=1;HaplotypeScore=0.2010;MQ=133.80;MQ0=0;MQRankSum=0.882;MQRankSumZ=0.901;QD=6.50;ReadPosRankSum=0.136;ReadPosRankSumZ=1.867;SB=-40.24;VQSLOD=5.0100;set=ALL12		
21	33038347	rs8133032	C	A	12406.86	PASS	AC=249;AF=0.3588;AN=694;BaseQRankSum=0.000;BaseQRankSumZ=16.677;DB;DP=1539;Dels=0.00;HRun=0;HaplotypeScore=0.3167;MQ=45.53;MQ0=121;MQRankSum=60.083;MQRankSumZ=-4.757;QD=17.50;ReadPosRankSum=0.790;ReadPosRankSumZ=0.969;SB=-6458.15;VQSLOD=5.4291;set=ALL12		
21	33038402	.	A	T	136.06	PASS	AC=4;AF=0.0041;AN=980;BaseQRankSum=13.835;BaseQRankSumZ=-1.735;DP=2343;Dels=0.00;HRun=0;HaplotypeScore=0.2268;MQ=56.86;MQ0=91;MQRankSum=11.279;MQRankSumZ=-1.443;QD=4.47;ReadPosRankSum=8.682;ReadPosRankSumZ=-1.101;SB=-26.80;VQSLOD=4.5783;set=ALL12		
21	33038432	.	G	A	104.73	PASS	AC=2;AF=0.0021;AN=956;BaseQRankSum=0.253;BaseQRankSumZ=1.584;DP=2298;Dels=0.00;HRun=0;HaplotypeScore=0.2471;MQ=58.79;MQ0=52;MQRankSum=0.068;MQRankSumZ=2.154;QD=9.29;ReadPosRankSum=2.204;ReadPosRankSumZ=0.259;SB=-11.13;VQSLOD=7.5784;set=ALL12		
21	33038566	.	T	A	70.32	PASS	AC=1;AF=0.0011;AN=872;BaseQRankSum=30.359;BaseQRankSumZ=-3.115;DP=2039;Dels=0.00;HRun=0;HaplotypeScore=0.4019;MQ=61.44;MQ0=9;MQRankSum=7.441;MQRankSumZ=-0.914;QD=8.53;ReadPosRankSum=4.249;ReadPosRankSumZ=-0.316;SB=-30.19;VQSLOD=5.0536;set=ALL12		
21	33038575	.	C	G	103.01	PASS	AC=1;AF=0.0015;AN=686;BaseQRankSum=0.068;BaseQRankSumZ=2.155;DP=1685;Dels=0.00;HRun=0;HaplotypeScore=0.3761;MQ=73.22;MQ0=6;MQRankSum=0.128;MQRankSumZ=1.894;QD=12.69;ReadPosRankSum=0.086;ReadPosRankSumZ=2.060;SB=-59.76;VQSLOD=5.8494;set=ALL12		
21	33038581	.	C	T	125.21	PASS	AC=1;AF=0.0021;AN=468;BaseQRankSum=0.028;BaseQRankSumZ=2.486;DP=1182;Dels=0.00;HRun=1;HaplotypeScore=0.2024;MQ=80.82;MQ0=2;MQRankSum=3.365;MQRankSumZ=-0.098;QD=13.75;ReadPosRankSum=4.209;ReadPosRankSumZ=-0.307;SB=-73.95;VQSLOD=6.4777;set=ALL12		
21	33038629	.	G	C	62.79	PASS	AC=3;AF=0.0033;AN=910;BaseQRankSum=2.262;BaseQRankSumZ=0.238;DP=2407;Dels=0.00;HRun=0;HaplotypeScore=0.3390;MQ=97.61;MQ0=1;MQRankSum=0.289;MQRankSumZ=1.519;QD=3.78;ReadPosRankSum=4.582;ReadPosRankSumZ=-0.390;SB=-62.50;VQSLOD=5.7429;set=ALL12		
21	33038675	rs17883998	T	C	26.48	PASS	AC=2;AF=0.0028;AN=712;BaseQRankSum=46.773;BaseQRankSumZ=-4.096;DB;DP=2297;Dels=0.00;HRun=0;HaplotypeScore=0.2496;MQ=116.23;MQ0=0;MQRankSum=0.459;MQRankSumZ=1.279;QD=2.31;ReadPosRankSum=3.421;ReadPosRankSumZ=-0.113;SB=-33.44;VQSLOD=3.9863;set=ALL12		
21	33038706	rs77112488	T	C	35.41	PASS	AC=1;AF=0.0011;AN=922;BaseQRankSum=45.224;BaseQRankSumZ=-4.013;DB;DP=2708;Dels=0.00;HRun=0;HaplotypeScore=0.2669;MQ=110.31;MQ0=0;MQRankSum=1.928;MQRankSumZ=0.363;QD=2.77;ReadPosRankSum=13.722;ReadPosRankSumZ=-1.723;SB=-44.29;VQSLOD=3.4889;set=ALL12		
21	33038742	rs17885833	T	C	486.79	PASS	AC=14;AF=0.0198;AN=706;BaseQRankSum=42.326;BaseQRankSumZ=-3.852;DB;DP=2206;Dels=0.00;HRun=0;HaplotypeScore=0.3455;MQ=93.07;MQ0=0;MQRankSum=3.071;MQRankSumZ=-0.018;QD=5.59;ReadPosRankSum=2.235;ReadPosRankSumZ=0.247;SB=-286.04;VQSLOD=7.4185;set=ALL12		
21	33038865	rs2234694	A	C	1613.49	PASS	AC=41;AF=0.03748;AN=1094;BaseQRankSum=37.041;BaseQRankSumZ=-3.543;DB;DP=2954;Dels=0.00;HRun=0;HaplotypeScore=0.2216;MQ=125.87;MQ0=0;MQRankSum=0.000;MQRankSumZ=5.680;QD=9.17;ReadPosRankSum=5.774;ReadPosRankSumZ=-0.629;SB=-845.36;VQSLOD=6.8505;set=ALL12		
21	33039038	.	C	T	39.80	PASS	AC=1;AF=0.0021;AN=474;BaseQRankSum=0.345;BaseQRankSumZ=1.430;DP=1552;Dels=0.00;HRun=0;HaplotypeScore=0.2110;MQ=128.07;MQ0=1;MQRankSum=0.091;MQRankSumZ=2.039;QD=6.42;ReadPosRankSum=4.681;ReadPosRankSumZ=-0.412;SB=-28.85;VQSLOD=6.3132;set=ALL12		
21	33039039	rs77319474	G	A	603.88	PASS	AC=7;AF=0.0100;AN=700;BaseQRankSum=0.000;BaseQRankSumZ=4.253;DB;DP=2160;Dels=0.00;HRun=1;HaplotypeScore=0.2274;MQ=124.46;MQ0=1;MQRankSum=0.804;MQRankSumZ=0.958;QD=11.60;ReadPosRankSum=15.660;ReadPosRankSumZ=-1.924;SB=-382.44;VQSLOD=5.9735;set=ALL12		
21	33039074	rs17885634	A	G	2431.15	PASS	AC=41;AF=0.0581;AN=706;BaseQRankSum=200.000;BaseQRankSumZ=-8.758;DB;DP=2227;Dels=0.00;HRun=0;HaplotypeScore=0.2769;MQ=127.91;MQ0=1;MQRankSum=0.207;MQRankSumZ=1.680;QD=9.69;ReadPosRankSum=3.771;ReadPosRankSumZ=-0.203;SB=-1395.24;VQSLOD=8.0940;set=ALL12		
21	33039206	.	G	A	69.09	PASS	AC=1;AF=0.0022;AN=462;BaseQRankSum=1.933;BaseQRankSumZ=0.360;DP=1312;Dels=0.00;HRun=1;HaplotypeScore=0.2873;MQ=81.26;MQ0=0;MQRankSum=2.964;MQRankSumZ=0.013;QD=8.48;ReadPosRankSum=0.954;ReadPosRankSumZ=0.852;SB=10.42;VQSLOD=6.1068;set=ALL12		
21	33039320	rs2070424	A	G	24954.10	PASS	AC=342;AF=0.3717;AN=920;BaseQRankSum=200.000;BaseQRankSumZ=-30.144;DB;DP=2641;Dels=0.00;HRun=1;HaplotypeScore=0.2593;MQ=100.91;MQ0=0;MQRankSum=1.048;MQRankSumZ=0.791;QD=17.89;ReadPosRankSum=7.647;ReadPosRankSumZ=-0.947;SB=-11677.59;VQSLOD=8.2996;set=ALL12		
21	33039407	.	A	G	56.73	PASS	AC=2;AF=0.0022;AN=918;BaseQRankSum=38.980;BaseQRankSumZ=-3.659;DP=2707;Dels=0.00;HRun=0;HaplotypeScore=0.2312;MQ=103.38;MQ0=0;MQRankSum=0.150;MQRankSumZ=1.826;QD=4.82;ReadPosRankSum=15.473;ReadPosRankSumZ=-1.905;SB=-49.16;VQSLOD=5.4854;set=ALL12		
21	33039506	rs112989936	C	G	71.54	PASS	AC=1;AF=0.0014;AN=712;BaseQRankSum=1.525;BaseQRankSumZ=0.535;DB;DP=2398;Dels=0.00;HRun=1;HaplotypeScore=0.2437;MQ=113.13;MQ0=0;MQRankSum=1.282;MQRankSumZ=0.657;QD=13.97;ReadPosRankSum=0.049;ReadPosRankSumZ=2.281;SB=-33.16;VQSLOD=6.4672;set=ALL12		
21	33039603	rs80265967	A	C	24.77	PASS	AC=2;AF=0.00182;AN=1098;BaseQRankSum=25.046;BaseQRankSumZ=-2.734;DB;DP=3075;Dels=0.00;HRun=1;HaplotypeScore=0.2198;MQ=109.71;MQ0=0;MQRankSum=1.046;MQRankSumZ=0.792;QD=2.37;ReadPosRankSum=26.239;ReadPosRankSumZ=-2.823;SB=-53.89;VQSLOD=1.4722;set=ALL12		
21	33039697	rs17886692	T	C	29.04	PASS	AC=1;AF=0.0014;AN=708;BaseQRankSum=8.007;BaseQRankSumZ=-1.002;DB;DP=2383;Dels=0.00;HRun=1;HaplotypeScore=0.2946;MQ=112.32;MQ0=0;MQRankSum=1.355;MQRankSumZ=0.619;QD=3.42;ReadPosRankSum=2.986;ReadPosRankSumZ=0.007;SB=-21.09;VQSLOD=4.0609;set=ALL12		
21	33039826	.	T	C	202.24	PASS	AC=2;AF=0.0022;AN=920;BaseQRankSum=7.572;BaseQRankSumZ=-0.935;DP=2893;Dels=0.00;HRun=0;HaplotypeScore=0.2522;MQ=106.98;MQ0=0;MQRankSum=1.566;MQRankSumZ=0.517;QD=14.13;ReadPosRankSum=0.172;ReadPosRankSumZ=1.766;SB=-122.88;VQSLOD=7.0813;set=ALL12		
21	33039917	rs76734991	C	T	222.22	PASS	AC=3;AF=0.0042;AN=706;BaseQRankSum=0.213;BaseQRankSumZ=1.666;DB;DP=2383;Dels=0.00;HRun=0;HaplotypeScore=0.2944;MQ=110.98;MQ0=0;MQRankSum=1.357;MQRankSumZ=0.618;QD=9.43;ReadPosRankSum=14.595;ReadPosRankSumZ=-1.816;SB=-113.05;VQSLOD=6.9997;set=ALL12		
21	33040004	rs17883234	T	G	5560.85	PASS	AC=59;AF=0.0831;AN=710;BaseQRankSum=200.000;BaseQRankSumZ=-8.918;DB;DP=2159;Dels=0.00;HRun=1;HaplotypeScore=0.2361;MQ=104.25;MQ0=0;MQRankSum=0.368;MQRankSumZ=1.397;QD=16.55;ReadPosRankSum=4.620;ReadPosRankSumZ=-0.398;SB=-2452.79;VQSLOD=7.9589;set=ALL12		
21	33040029	rs4816407	A	G	26743.14	PASS	AC=339;AF=0.3758;AN=902;BaseQRankSum=200.000;BaseQRankSumZ=-12.109;DB;DP=2508;Dels=0.00;HRun=0;HaplotypeScore=0.2392;MQ=99.48;MQ0=0;MQRankSum=1.852;MQRankSumZ=0.393;QD=19.68;ReadPosRankSum=3.058;ReadPosRankSumZ=-0.014;SB=-12851.21;VQSLOD=9.1154;set=ALL12		
21	33040063	rs117466144	T	C	146.65	PASS	AC=2;AF=0.0022;AN=910;BaseQRankSum=51.071;BaseQRankSumZ=-4.320;DB;DP=2676;Dels=0.00;HRun=1;HaplotypeScore=0.1259;MQ=98.10;MQ0=0;MQRankSum=6.326;MQRankSumZ=-0.729;QD=5.92;ReadPosRankSum=12.984;ReadPosRankSumZ=-1.642;SB=-107.12;VQSLOD=5.1038;set=ALL12		
21	33040157	rs17881732	C	A	1043.56	PASS	AC=21;AF=0.01892;AN=1110;BaseQRankSum=0.001;BaseQRankSumZ=3.652;DB;DP=2922;Dels=0.00;HRun=4;HaplotypeScore=0.2452;MQ=119.75;MQ0=0;MQRankSum=0.288;MQRankSumZ=1.521;QD=9.40;ReadPosRankSum=2.204;ReadPosRankSumZ=0.258;SB=-596.32;VQSLOD=5.7364;set=ALL12		
21	33040162	rs1041740	C	T	26489.58	PASS	AC=327;AF=0.29781;AN=1098;BaseQRankSum=0.000;BaseQRankSumZ=7.352;DB;DP=2890;Dels=0.00;HRun=0;HaplotypeScore=0.2256;MQ=117.51;MQ0=0;MQRankSum=0.003;MQRankSumZ=3.158;QD=17.75;ReadPosRankSum=2.055;ReadPosRankSumZ=0.314;SB=-11836.43;VQSLOD=9.4241;set=ALL12		
21	33040357	.	C	T	9.08	PASS	AC=1;AF=0.00094;AN=1064;BaseQRankSum=2.704;BaseQRankSumZ=0.092;DP=2903;Dels=0.00;HRun=2;HaplotypeScore=0.1600;MQ=126.72;MQ0=1;MQRankSum=0.478;MQRankSumZ=1.258;QD=0.90;ReadPosRankSum=5.706;ReadPosRankSumZ=-0.617;SB=-32.22;VQSLOD=0.0906;set=ALL12		
21	33040365	.	T	C	96.50	PASS	AC=1;AF=0.0014;AN=704;BaseQRankSum=28.724;BaseQRankSumZ=-3.002;DP=2170;Dels=0.00;HRun=0;HaplotypeScore=0.2562;MQ=120.42;MQ0=0;MQRankSum=0.007;MQRankSumZ=2.935;QD=5.92;ReadPosRankSum=3.098;ReadPosRankSumZ=-0.025;SB=-43.82;VQSLOD=6.6750;set=ALL12		
21	33040371	rs4817420	C	T	28773.95	PASS	AC=314;AF=0.3466;AN=906;BaseQRankSum=0.000;BaseQRankSumZ=28.404;DB;DP=2570;Dels=0.00;HRun=0;HaplotypeScore=0.1801;MQ=118.18;MQ0=0;MQRankSum=1.564;MQRankSumZ=0.517;QD=20.94;ReadPosRankSum=7.816;ReadPosRankSumZ=-0.973;SB=-13708.63;VQSLOD=8.8380;set=ALL12		
21	33040475	.	G	T	106.80	PASS	AC=4;AF=0.0057;AN=702;BaseQRankSum=11.629;BaseQRankSumZ=-1.485;DP=1931;Dels=0.00;HRun=0;HaplotypeScore=0.2383;MQ=113.98;MQ0=0;MQRankSum=1.017;MQRankSumZ=0.811;QD=4.64;ReadPosRankSum=9.348;ReadPosRankSumZ=-1.194;SB=-73.64;VQSLOD=6.4553;set=ALL12		
21	33040497	.	G	A	37.72	PASS	AC=1;AF=0.0011;AN=912;BaseQRankSum=0.032;BaseQRankSumZ=2.439;DP=2522;Dels=0.00;HRun=1;HaplotypeScore=0.1909;MQ=121.04;MQ0=0;MQRankSum=26.178;MQRankSumZ=-2.819;QD=3.94;ReadPosRankSum=2.645;ReadPosRankSumZ=0.110;SB=9.95;VQSLOD=2.9614;set=ALL12		
21	33040511	rs17884462	G	A	369.86	PASS	AC=7;AF=0.0099;AN=710;BaseQRankSum=0.000;BaseQRankSumZ=4.376;DB;DP=2058;Dels=0.00;HRun=0;HaplotypeScore=0.2157;MQ=123.67;MQ0=0;MQRankSum=0.509;MQRankSumZ=1.223;QD=7.47;ReadPosRankSum=5.057;ReadPosRankSumZ=-0.490;SB=-253.34;VQSLOD=8.2338;set=ALL12		
21	33040596	rs17880044	T	C	164.41	PASS	AC=2;AF=0.0028;AN=710;BaseQRankSum=5.876;BaseQRankSumZ=-0.648;DB;DP=2223;Dels=0.00;HRun=0;HaplotypeScore=0.2127;MQ=129.10;MQ0=0;MQRankSum=0.039;MQRankSumZ=2.368;QD=10.58;ReadPosRankSum=3.780;ReadPosRankSumZ=-0.205;SB=-46.08;VQSLOD=8.2957;set=ALL12		
21	33040654	rs117304270	G	C	234.39	PASS	AC=5;AF=0.00460;AN=1088;BaseQRankSum=1.003;BaseQRankSumZ=0.819;DB;DP=2669;Dels=0.00;HRun=0;HaplotypeScore=0.1669;MQ=107.46;MQ0=0;MQRankSum=0.995;MQRankSumZ=0.825;QD=8.37;ReadPosRankSum=15.684;ReadPosRankSumZ=-1.927;SB=-172.15;VQSLOD=6.5007;set=ALL12		
21	33041044	.	T	G	11.35	TruthSensitivityTranche99.90to100.00	AC=1;AF=0.00093;AN=1076;BaseQRankSum=33.026;BaseQRankSumZ=-3.292;DP=3001;Dels=0.00;HRun=1;HaplotypeScore=0.1376;MQ=99.05;MQ0=0;MQRankSum=8.531;MQRankSumZ=-1.079;QD=0.97;ReadPosRankSum=4.397;ReadPosRankSumZ=-0.350;SB=19.32;VQSLOD=-2.0133;set=ALL12		
21	33041208	.	T	C	85.73	PASS	AC=1;AF=0.0014;AN=700;BaseQRankSum=16.610;BaseQRankSumZ=-2.017;DP=2043;Dels=0.00;HRun=0;HaplotypeScore=0.1652;MQ=114.63;MQ0=0;MQRankSum=0.497;MQRankSumZ=1.236;QD=6.90;ReadPosRankSum=1.670;ReadPosRankSumZ=0.470;SB=3.96;VQSLOD=6.9109;set=ALL12		
21	33041230	rs17880487	C	T	2112.53	PASS	AC=41;AF=0.0445;AN=922;BaseQRankSum=0.006;BaseQRankSumZ=2.977;DB;DP=2471;Dels=0.00;HRun=0;HaplotypeScore=0.1509;MQ=110.68;MQ0=0;MQRankSum=1.954;MQRankSumZ=0.352;QD=10.67;ReadPosRankSum=5.272;ReadPosRankSumZ=-0.533;SB=-1384.52;VQSLOD=8.0599;set=ALL12		
21	33041263	.	T	A	150.88	PASS	AC=4;AF=0.00375;AN=1068;BaseQRankSum=6.590;BaseQRankSumZ=-0.775;DP=2901;Dels=0.00;HRun=1;HaplotypeScore=0.1260;MQ=122.78;MQ0=0;MQRankSum=2.007;MQRankSumZ=0.332;QD=6.29;ReadPosRankSum=1.324;ReadPosRankSumZ=0.635;SB=-118.92;VQSLOD=5.6508;set=ALL12		
21	33041352	.	A	T	86.23	PASS	AC=1;AF=0.0014;AN=706;BaseQRankSum=34.484;BaseQRankSumZ=-3.385;DP=1980;Dels=0.00;HRun=1;HaplotypeScore=0.1724;MQ=102.40;MQ0=0;MQRankSum=1.572;MQRankSumZ=0.514;QD=12.07;ReadPosRankSum=4.065;ReadPosRankSumZ=-0.274;SB=0.74;VQSLOD=5.9545;set=ALL12		
21	33041504	.	G	A	5.97	TruthSensitivityTranche99.89to99.90	AC=1;AF=0.00092;AN=1082;BaseQRankSum=19.315;BaseQRankSumZ=-2.267;DP=3147;Dels=0.00;HRun=0;HaplotypeScore=0.1720;MQ=118.38;MQ0=0;MQRankSum=3.775;MQRankSumZ=-0.204;QD=0.94;ReadPosRankSum=10.982;ReadPosRankSumZ=-1.407;SB=6.17;VQSLOD=-1.7881;set=ALL12		
21	33041560	.	A	C	20.75	PASS	AC=1;AF=0.0011;AN=920;BaseQRankSum=34.718;BaseQRankSumZ=-3.400;DP=2555;Dels=0.00;HRun=1;HaplotypeScore=0.1899;MQ=116.04;MQ0=1;MQRankSum=0.998;MQRankSumZ=0.823;QD=2.32;ReadPosRankSum=18.554;ReadPosRankSumZ=-2.199;SB=-15.91;VQSLOD=0.4337;set=ALL12		
