##fileformat=VCFv4.1
##FILTER=<ID=LowQual,Description="Low quality">
##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=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,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="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="Filtered 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=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##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=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
##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="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="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[test_trio/reads.10462.recal.bam] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[./test_trio/Target_Intervals/chr22_target_interval.bed] excludeIntervals=null reference_sequence=reference_genome/HGC/Homo_sapiens_GRCh37_53.fasta rodBind=[] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false downsampling_type=null downsample_to_fraction=null downsample_to_coverage=1000 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 genotype_likelihoods_model=SNP p_nonref_model=EXACT heterozygosity=0.001 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=50.0 standard_min_confidence_threshold_for_emitting=10.0 computeSLOD=false alleles=(RodBinding name= source=UNBOUND) 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 getGapPenaltiesFromData=false indel_recal_file=indel.recal_data.csv indelDebug=false dovit=false GSA_PRODUCTION_ONLY=false exactCalculation=LINEAR_EXPERIMENTAL ignoreSNPAlleles=false output_all_callable_bases=false genotype=false dbsnp=(RodBinding name=dbsnp source=DBsnp/b37/dbsnp_132_b37_sanger.vcf) 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=[]"
##VariantAnnotator="analysis_type=VariantAnnotator input_file=[test_trio/reads.10462.recal.bam] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[./test_trio/Target_Intervals/chr22_target_interval.bed] excludeIntervals=null reference_sequence=reference_genome/HGC/Homo_sapiens_GRCh37_53.fasta rodBind=[] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false 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 variant=(RodBinding name=variant source=test_trio/SNP/chr22_new_snp.vcf) snpEffFile=(RodBinding name= source=UNBOUND) dbsnp=(RodBinding name=dbsnp source=DBsnp/b37/dbsnp_132_b37_sanger.vcf) comp=[] resource=[] 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 annotation=[HaplotypeScore, FisherStrand, MappingQualityRankSumTest, ReadPosRankSumTest, RMSMappingQuality, DepthOfCoverage, QualByDepth] group=[] expression=[] useAllAnnotations=false list=false assume_single_sample_reads=null vcfContainsOnlyIndels=false"
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##reference=file:///home/elliott/reference_genome/HGC/Homo_sapiens_GRCh37_53.fasta
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	DNMSCZ5100233
Chr22	16256352	.	T	C	43.79	LowQual	AC=1;AF=0.50;AN=2;BaseQRankSum=4.023;DP=347;Dels=0.00;HRun=0;HaplotypeScore=0.0000;MQ=4.05;MQ0=318;MQRankSum=-0.337;QD=0.13;ReadPosRankSum=0.652	GT:AD:DP:GQ:PL	0/1:172,175:347:50.10:74,0,50
Chr22	16256430	.	A	G	497.21	PASS	AC=1;AF=0.50;AN=2;BaseQRankSum=-7.858;DP=533;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.6651;MQ=8.27;MQ0=352;MQRankSum=-1.257;QD=0.93;ReadPosRankSum=-0.856	GT:AD:DP:GQ:PL	0/1:262,269:533:99:527,0,341
Chr22	16256512	.	T	C	1320.63	PASS	AC=1;AF=0.50;AN=2;BaseQRankSum=13.097;DP=664;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=10.0005;MQ=10.83;MQ0=292;MQRankSum=0.422;QD=1.99;ReadPosRankSum=-0.094	GT:AD:DP:GQ:PL	0/1:295,369:664:99:1351,0,697
Chr22	16269934	.	A	G	775.82	PASS	AC=1;AF=0.50;AN=2;BaseQRankSum=7.474;DP=834;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.9774;MQ=11.52;MQ0=601;MQRankSum=-1.915;QD=0.93;ReadPosRankSum=-0.117	GT:AD:DP:GQ:PL	0/1:578,248:826:99:806,0,2272
Chr22	16449050	.	G	A	2505.21	PASS	AC=1;AF=0.50;AN=2;BaseQRankSum=-11.133;DP=458;Dels=0.00;FS=2.911;HRun=0;HaplotypeScore=10.2021;MQ=17.69;MQ0=157;MQRankSum=2.263;QD=5.47;ReadPosRankSum=-2.541	GT:AD:DP:GQ:PL	0/1:264,190:458:99:2535,0,2578
Chr22	17072483	rs2236639	A	G	5024.23	PASS	AC=2;AF=1.00;AN=2;DB;DP=196;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=5.2075;MQ=34.43;MQ0=17;QD=25.63	GT:AD:DP:GQ:PL	1/1:0,196:196:99:5022,466,0
Chr22	17073066	rs5747988	A	G	1309.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=1.3670;MQ=56.27;MQ0=0;QD=28.47	GT:AD:DP:GQ:PL	1/1:0,46:46:99:1342,123,0
Chr22	17082913	.	A	C	17.96	LowQual	AC=1;AF=0.50;AN=2;BaseQRankSum=-0.467;DP=14;Dels=0.00;HRun=6;HaplotypeScore=0.8321;MQ=56.27;MQ0=0;MQRankSum=0.467;QD=1.28;ReadPosRankSum=-1.557	GT:AD:DP:GQ:PL	0/1:11,3:14:47.88:48,0,203
Chr22	17128089	rs76160126	G	A	886.26	PASS	AC=1;AF=0.50;AN=2;BaseQRankSum=-5.036;DB;DP=115;Dels=0.00;FS=3.900;HRun=0;HaplotypeScore=1.7356;MQ=29.84;MQ0=22;MQRankSum=-0.327;QD=7.71;ReadPosRankSum=-0.235	GT:AD:DP:GQ:PL	0/1:68,47:115:99:916,0,1008
Chr22	17156061	rs8142573	A	G	2153.94	PASS	AC=1;AF=0.50;AN=2;BaseQRankSum=7.543;DB;DP=236;Dels=0.00;FS=0.552;HRun=0;HaplotypeScore=5.3265;MQ=38.54;MQ0=21;MQRankSum=0.638;QD=9.13;ReadPosRankSum=-1.070	GT:AD:DP:GQ:PL	0/1:146,90:236:99:2184,0,3255
Chr22	17156280	rs6518594	A	G	10658.69	PASS	AC=2;AF=1.00;AN=2;DB;DP=319;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=4.1983;MQ=57.22;MQ0=0;QD=33.41	GT:AD:DP:GQ:PL	1/1:0,319:319:99:10657,885,0
Chr22	17446991	rs4819925	C	T	4098.66	PASS	AC=2;AF=1.00;AN=2;DB;DP=112;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=1.6671;MQ=59.79;MQ0=0;QD=36.60	GT:AD:DP:GQ:PL	1/1:0,112:112:99:4098,325,0
Chr22	17469026	rs5992604	G	A	467.43	PASS	AC=1;AF=0.50;AN=2;BaseQRankSum=-0.866;DB;DP=37;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=2.7035;MQ=59.25;MQ0=0;MQRankSum=-1.960;QD=12.63;ReadPosRankSum=-0.471	GT:AD:DP:GQ:PL	0/1:19,18:37:99:497,0,490
Chr22	17469049	rs28502153	C	A	380.12	PASS	AC=1;AF=0.50;AN=2;BaseQRankSum=-3.164;DB;DP=29;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.9832;MQ=59.04;MQ0=0;MQRankSum=0.851;QD=13.11;ReadPosRankSum=1.942	GT:AD:DP:GQ:PL	0/1:14,15:29:99:410,0,424
Chr22	17539625	rs1054946	C	G	14.92	LowQual	AC=1;AF=0.50;AN=2;DB;DP=2;Dels=0.00;HRun=0;HaplotypeScore=0.0000;MQ=60.00;MQ0=0;QD=7.46	GT:AD:DP:GQ:PL	0/1:0,2:2:1.76:45,3,0
Chr22	17565932	rs917864	T	C	36.72	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;HRun=0;HaplotypeScore=0.0000;MQ=60.00;MQ0=0;QD=18.36	GT:AD:DP:GQ:PL	1/1:0,2:2:6.01:68,6,0
Chr22	17565974	rs917865	G	C	41.87	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;HRun=2;HaplotypeScore=0.0000;MQ=60.00;MQ0=0;QD=20.93	GT:AD:DP:GQ:PL	1/1:0,2:2:6.02:73,6,0
Chr22	17586471	rs2241046	C	T	8817.64	PASS	AC=2;AF=1.00;AN=2;DB;DP=255;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=2.4658;MQ=58.63;MQ0=0;QD=34.58	GT:AD:DP:GQ:PL	1/1:0,255:255:99:8817,719,0
Chr22	17589209	rs879577	C	T	690.55	PASS	AC=1;AF=0.50;AN=2;BaseQRankSum=0.286;DB;DP=54;Dels=0.00;FS=1.114;HRun=0;HaplotypeScore=1.6281;MQ=60.00;MQ0=0;MQRankSum=0.684;QD=12.79;ReadPosRankSum=1.324	GT:AD:DP:GQ:PL	0/1:26,28:54:99:721,0,651
Chr22	17589567	rs879575	C	T	506.78	PASS	AC=1;AF=0.50;AN=2;BaseQRankSum=-3.799;DB;DP=32;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0000;MQ=60.00;MQ0=0;MQRankSum=-0.230;QD=15.84;ReadPosRankSum=0.729	GT:AD:DP:GQ:PL	0/1:13,19:32:99:537,0,380
Chr22	17590269	rs4819555	C	T	113.87	PASS	AC=1;AF=0.50;AN=2;BaseQRankSum=-0.800;DB;DP=15;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.5784;MQ=58.45;MQ0=0;MQRankSum=-1.200;QD=7.59;ReadPosRankSum=0.533	GT:AD:DP:GQ:PL	0/1:10,5:15:99:144,0,295
Chr22	17591973	rs887795	G	T	43.53	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;HRun=1;HaplotypeScore=0.0000;MQ=60.00;MQ0=0;QD=21.77	GT:AD:DP:GQ:PL	1/1:0,2:2:6.02:75,6,0
Chr22	17594216	rs9605216	A	G	10.43	LowQual	AC=1;AF=0.50;AN=2;DB;DP=1;Dels=0.00;HRun=1;HaplotypeScore=0.0000;MQ=60.00;MQ0=0;QD=10.43	GT:AD:DP:GQ:PL	0/1:0,1:1:1.76:40,3,0
Chr22	17596178	rs4819962	T	C	41.69	LowQual	AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;HRun=0;HaplotypeScore=0.0000;MQ=60.00;MQ0=0;QD=20.85	GT:AD:DP:GQ:PL	1/1:0,2:2:6.02:73,6,0
Chr22	17600148	rs9605220	A	G	510.49	PASS	AC=2;AF=1.00;AN=2;DB;DP=16;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0000;MQ=60.00;MQ0=0;QD=31.91	GT:AD:DP:GQ:PL	1/1:0,16:16:42.14:543,42,0
Chr22	17600977	rs5994165	G	A	921.06	PASS	AC=1;AF=0.50;AN=2;BaseQRankSum=4.317;DB;DP=62;Dels=0.00;FS=1.379;HRun=2;HaplotypeScore=0.0000;MQ=60.00;MQ0=0;MQRankSum=-0.472;QD=14.86;ReadPosRankSum=-0.416	GT:AD:DP:GQ:PL	0/1:30,32:62:99:951,0,761
Chr22	17630486	rs1034859	C	A	4985.79	PASS	AC=2;AF=1.00;AN=2;DB;DP=153;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=4.3875;MQ=59.06;MQ0=0;QD=32.59	GT:AD:DP:GQ:PL	1/1:1,152:153:99:4985,430,0