##fileformat=VCFv4.1
##FILTER=<ID=LowQual,Description="Low quality">
##FILTER=<ID=minDP,Description="DP < 140">
##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="Approximate read depth (reads with MQ=255 or	with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=MLPSAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for	the alternate allele count, in the same	order as listed, for each individual sample">
##FORMAT=<ID=MLPSAF,Number=A,Type=Float,Description="Maximum likelihood	expectation (MLE) for the alternate allele fraction, in	the same order as listed, for each individual sample">
##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="Approximate read depth; some reads may	have been filtered">
##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=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=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele	counts (not necessarily	the same as the	AC), for each ALT allele, in the same order as listed">
##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency	(not necessarily the same as the AF), for each ALT allele, in the same order as	listed">
##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=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat	unit is	repeated, for each allele (including reference)">
##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from	Wilcoxon rank sum test of Alt vs. Ref read position bias">
##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[realigned_BQSR.bam] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[] intervals=[targets_sorted_gatk.bed] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=genome.fa nonDeterministicRandomSeed=false disableRandomization=false maxRuntime=-1	maxRuntimeUnits=MINUTES	downsampling_type=NONE downsample_to_fraction=null downsample_to_coverage=null enable_experimental_downsampling=false baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6	defaultBaseQualities=-1	validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false	num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=BOTH pcr_error_rate=1.0E-4 computeSLOD=false annotateNDA=false pair_hmm_implementation=ORIGINAL min_base_quality_score=17 max_deletion_fraction=0.05 min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10 indelGapOpenPenalty=45	indelHaplotypeSize=80 indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null	sample_ploidy=4	min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false heterozygosity=0.001	genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=50.0 standard_min_confidence_threshold_for_emitting=30.0	alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 p_nonref_model=EXACT_INDEPENDENT contamination_fraction_to_filter=0.05 logRemovedReadsFromContaminationFiltering=null	exactcallslog=null dbsnp=(RodBinding name=dbsnp	source=dbsnp.vcf) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[]	filter_mismatching_base_and_quals=false"
##VariantFiltration="analysis_type=VariantFiltration input_file=[] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[] intervals=null	excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=genome.fa	nonDeterministicRandomSeed=false disableRandomization=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 enable_experimental_downsampling=false baq=OFF baqGapOpenPenalty=40.0 performanceLog=null	useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false	emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null	num_threads=1 num_cpu_threads_per_data_thread=1	num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[]	pedigreeString=[] pedigreeValidationType=STRICT	allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false	variant=(RodBinding name=variant source=variants.raw.vcf) mask=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub filterExpression=[DP <	140] filterName=[minDP]	genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3	clusterWindowSize=0 maskExtension=0 maskName=Mask missingValuesInExpressionsShouldEvaluateAsFailing=false invalidatePreviousFilters=false filter_mismatching_base_and_quals=false"
##contig=<ID=chrM,length=16571>
##contig=<ID=chr1,length=249250621>
##contig=<ID=chr2,length=243199373>
##contig=<ID=chr3,length=198022430>
##contig=<ID=chr4,length=191154276>
##contig=<ID=chr5,length=180915260>
##contig=<ID=chr6,length=171115067>
##contig=<ID=chr7,length=159138663>
##contig=<ID=chr8,length=146364022>
##contig=<ID=chr9,length=141213431>
##contig=<ID=chr10,length=135534747>
##contig=<ID=chr11,length=135006516>
##contig=<ID=chr12,length=133851895>
##contig=<ID=chr13,length=115169878>
##contig=<ID=chr14,length=107349540>
##contig=<ID=chr15,length=102531392>
##contig=<ID=chr16,length=90354753>
##contig=<ID=chr17,length=81195210>
##contig=<ID=chr18,length=78077248>
##contig=<ID=chr19,length=59128983>
##contig=<ID=chr20,length=63025520>
##contig=<ID=chr21,length=48129895>
##contig=<ID=chr22,length=51304566>
##contig=<ID=chrX,length=155270560>
##contig=<ID=chrY,length=59373566>
##reference=file://genome.fa
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	human1
chr2	179441386	rs67041405	G	A	11865.20	PASS	AC=2;AF=0.500;AN=4;BaseQRankSum=7.624;DB;DP=859;Dels=0.00;FS=2.010;HaplotypeScore=14.9569;MLEAC=2;MLEAF=0.500;MQ=58.56;MQ0=0;MQRankSum=0.294;QD=13.81;ReadPosRankSum=-1.136	GT:AD:DP:GQ:MLPSAC:MLPSAF:PL	0/0/1/1:481,376:858:99:2:0.500:11892,283,0,783,32767
chr2	179444768	rs4145333	C	G	28584.20	PASS	AC=4;AF=1.00;AN=4;DB;DP=732;Dels=0.00;FS=0.000;HaplotypeScore=11.5294;MLEAC=4;MLEAF=1.00;MQ=58.57;MQ0=0;QD=39.05	GT:AD:DP:GQ:MLPSAC:MLPSAF:PL	1/1/1/1:0,731:732:99:4:1.00:28611,4387,2194,911,0
chr2	179518344	.	A	G	30.21	LowQual	AC=1;AF=0.250;AN=4;BaseQRankSum=-0.834;DP=1029;Dels=0.00;FS=2.732;HaplotypeScore=17.1641;MLEAC=1;MLEAF=0.250;MQ=4.17;MQ0=974;MQRankSum=0.629;QD=0.03;ReadPosRankSum=1.127	GT:AD:DP:GQ:MLPSAC:MLPSAF:PL	0/0/0/1:1023,5:1029:28:1:0.250:57,0,28,85,32767
chr2	179522634	.	G	T	101.23	PASS	AC=1;AF=0.250;AN=4;BaseQRankSum=-0.367;DP=946;Dels=0.00;FS=0.000;HaplotypeScore=6.8818;MLEAC=1;MLEAF=0.250;MQ=5.12;MQ0=864;MQRankSum=2.476;QD=0.11;ReadPosRankSum=0.299	GT:AD:DP:GQ:MLPSAC:MLPSAF:PL	0/0/0/1:931,15:946:21:1:0.250:128,0,21,80,32767
chr2	179522639	.	A	T	31.20	LowQual	AC=1;AF=0.250;AN=4;BaseQRankSum=-0.480;DP=915;Dels=0.00;FS=0.000;HaplotypeScore=5.0212;MLEAC=1;MLEAF=0.250;MQ=5.25;MQ0=829;MQRankSum=2.095;QD=0.03;ReadPosRankSum=0.907	GT:AD:DP:GQ:MLPSAC:MLPSAF:PL	0/0/0/1:893,8:915:35:1:0.250:58,0,35,109,32767
chr2	179527289	.	A	G	59.20	PASS	AC=1;AF=0.250;AN=4;BaseQRankSum=2.781;DP=1597;Dels=0.00;FS=0.000;HaplotypeScore=1.8824;MLEAC=1;MLEAF=0.250;MQ=5.52;MQ0=1421;MQRankSum=2.720;QD=0.04;ReadPosRankSum=1.705	GT:AD:DP:GQ:MLPSAC:MLPSAF:PL	0/0/0/1:1585,12:1597:78:1:0.250:86,0,78,32767,32767
chr2	179527290	.	T	G	59.20	PASS	AC=1;AF=0.250;AN=4;BaseQRankSum=2.161;DP=1604;Dels=0.00;FS=0.000;HaplotypeScore=1.8824;MLEAC=1;MLEAF=0.250;MQ=5.50;MQ0=1429;MQRankSum=2.640;QD=0.04;ReadPosRankSum=1.731	GT:AD:DP:GQ:MLPSAC:MLPSAF:PL	0/0/0/1:1587,15:1604:78:1:0.250:86,0,78,32767,32767
chr2	179527294	.	T	A	64.20	PASS	AC=1;AF=0.250;AN=4;BaseQRankSum=2.126;DP=1573;Dels=0.00;FS=0.000;HaplotypeScore=3.7069;MLEAC=1;MLEAF=0.250;MQ=5.38;MQ0=1410;MQRankSum=2.443;QD=0.04;ReadPosRankSum=0.937	GT:AD:DP:GQ:MLPSAC:MLPSAF:PL	0/0/0/1:1553,15:1573:71:1:0.250:91,0,71,32767,32767
chr3	183212026	rs2256061	C	T	8637.20	PASS	AC=2;AF=0.500;AN=4;BaseQRankSum=4.216;DB;DP=550;Dels=0.00;FS=0.308;HaplotypeScore=21.6098;MLEAC=2;MLEAF=0.500;MQ=58.16;MQ0=0;MQRankSum=0.240;QD=15.70;ReadPosRankSum=0.169	GT:AD:DP:GQ:MLPSAC:MLPSAF:PL	0/0/1/1:277,272:550:99:2:0.500:8664,334,0,348,32767
chr3	193854166	.	G	A	95.20	minDP	AC=1;AF=0.250;AN=4;BaseQRankSum=-3.033;DP=118;Dels=0.00;FS=20.110;HaplotypeScore=22.3088;MLEAC=1;MLEAF=0.250;MQ=57.10;MQ0=1;MQRankSum=0.396;QD=0.81;ReadPosRankSum=-3.779	GT:AD:DP:GQ:MLPSAC:MLPSAF:PL	0/0/0/1:103,15:118:99:1:0.250:122,0,147,32767,32767
chr3	195505829	.	G	A	438.20	PASS	AC=1;AF=0.250;AN=4;BaseQRankSum=-7.766;DP=356;Dels=0.00;FS=73.485;HaplotypeScore=110.3958;MLEAC=1;MLEAF=0.250;MQ=42.47;MQ0=15;MQRankSum=-6.492;QD=1.23;ReadPosRankSum=5.637	GT:AD:DP:GQ:MLPSAC:MLPSAF:PL	0/0/0/1:307,49:356:99:1:0.250:465,0,377,32767,32767
chr3	195505844	.	T	A	243.20	PASS	AC=1;AF=0.250;AN=4;BaseQRankSum=-5.296;DP=296;Dels=0.00;FS=85.599;HaplotypeScore=119.8613;MLEAC=1;MLEAF=0.250;MQ=39.90;MQ0=15;MQRankSum=-4.151;QD=0.82;ReadPosRankSum=3.513	GT:AD:DP:GQ:MLPSAC:MLPSAF:PL	0/0/0/1:269,26:296:99:1:0.250:270,0,325,32767,32767
chr5	149497177	rs246391	T	C	1703.20	minDP	AC=2;AF=0.500;AN=4;BaseQRankSum=4.298;DB;DP=126;Dels=0.00;FS=1.524;HaplotypeScore=0.0000;MLEAC=2;MLEAF=0.500;MQ=57.74;MQ0=0;MQRankSum=1.112;QD=13.52;ReadPosRankSum=0.493	GT:AD:DP:GQ:MLPSAC:MLPSAF:PL	0/0/1/1:70,56:126:45:2:0.500:1730,45,0,112,32767
chr5	149499672	rs246395	T	C	3855.20	PASS	AC=2;AF=0.500;AN=4;BaseQRankSum=8.641;DB;DP=300;Dels=0.00;FS=0.000;HaplotypeScore=6.5904;MLEAC=2;MLEAF=0.500;MQ=59.11;MQ0=0;MQRankSum=0.521;QD=12.85;ReadPosRankSum=1.438	GT:AD:DP:GQ:MLPSAC:MLPSAF:PL	0/0/1/1:178,122:300:56:2:0.500:3882,56,0,317,32767
chr5	159992655	.	T	C	5161.20	PASS	AC=2;AF=0.500;AN=4;BaseQRankSum=10.575;DB;DP=285;Dels=0.00;FS=2.584;HaplotypeScore=10.5702;MLEAC=2;MLEAF=0.500;MQ=58.37;MQ0=0;MQRankSum=1.513;QD=18.11;ReadPosRankSum=-0.170	GT:AD:DP:GQ:MLPSAC:MLPSAF:PL	0/0/1/1:132,153:285:99:2:0.500:5188,232,0,122,32767
chr5	159992754	.	T	G	6278.20	PASS	AC=2;AF=0.500;AN=4;BaseQRankSum=9.812;DB;DP=345;Dels=0.00;FS=9.222;HaplotypeScore=15.5061;MLEAC=2;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=-0.972;QD=18.20;ReadPosRankSum=-0.966	GT:AD:DP:GQ:MLPSAC:MLPSAF:PL	0/0/1/1:159,186:345:99:2:0.500:6305,288,0,130,32767
chrX	38146005	.	T	A	58.98	minDP	AC=2;AF=0.500;AN=4;BaseQRankSum=0.000;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=5.9263;MLEAC=1;MLEAF=0.250;MQ=37.20;MQ0=0;MQRankSum=-1.026;QD=8.43;ReadPosRankSum=0.000	GT:AD:DP:GQ:MLPSAC:MLPSAF:PL	0/0/1/1:2,2:7:3:2:0.500:56,3,0,3,65
chrX	39933339	.	A	G	10095.20	PASS	AC=4;AF=1.00;AN=4;BaseQRankSum=1.644;DB;DP=276;Dels=0.00;FS=3.337;HaplotypeScore=5.9456;MLEAC=4;MLEAF=1.00;MQ=58.73;MQ0=0;MQRankSum=1.694;QD=36.58;ReadPosRankSum=1.255	GT:AD:DP:GQ:MLPSAC:MLPSAF:PL	1/1/1/1:1,275:276:99:4:1.00:10122,1625,803,323,0
chrX	44921996	.	G	A	7412.20	PASS	AC=4;AF=1.00;AN=4;DB;DP=208;Dels=0.00;FS=0.000;HaplotypeScore=5.9749;MLEAC=4;MLEAF=1.00;MQ=58.59;MQ0=1;QD=35.64	GT:AD:DP:GQ:MLPSAC:MLPSAF:PL	1/1/1/1:0,207:208:99:4:1.00:7439,1233,617,256,0