##fileformat=VCFv4.2
##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
##FILTER=<ID=LowQual,Description="Low quality">
##FILTER=<ID=PASS,Description="All filters passed">
##FORMAT=<ID=AD,Number=R,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=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
##GATKCommandLine=<ID=HaplotypeCaller,Version=3.1-1-g07a4bf8,Date="Fri Apr 04 09:42:24 EDT 2014",Epoch=1396618944211,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/seq/external-data/1kg/GBR/exome/HG00141/HG00141.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=[/seq/picardtemp3/seq/sample_vcf/1kg_GBR/Exome/Homo_sapiens_assembly19/7d4759a5-8e11-324c-8d3a-cc375e53e06c/scattered/temp_0001_of_10/scattered.intervals] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=true 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 variant_index_type=LINEAR variant_index_parameter=128000 logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN graphOutput=null bamOutput=null bam_compression=null disable_bam_indexing=null generate_md5=null simplifyBAM=null bamWriterType=CALLED_HAPLOTYPES dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[ClippingRankSumTest, DepthPerSampleHC, StrandBiasBySample] excludeAnnotation=[SpanningDeletions, TandemRepeatAnnotator, ChromosomeCounts, FisherStrand, QualByDepth] heterozygosity=0.001 indel_heterozygosity=1.25E-4 genotyping_mode=DISCOVERY standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=3 input_prior=[] contamination_fraction_to_filter=0.019 contamination_fraction_per_sample_file=null p_nonref_model=EXACT_INDEPENDENT exactcallslog=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false numPruningSamples=1 recoverDanglingHeads=false dontRecoverDanglingTails=false consensus=false emitRefConfidence=GVCF GVCFGQBands=[5, 20, 60] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 minPruning=3 gcpHMM=10 includeUmappedReads=false useAllelesTrigger=false useFilteredReadsForAnnotations=false phredScaledGlobalReadMismappingRate=45 maxNumHaplotypesInPopulation=200 mergeVariantsViaLD=false pair_hmm_implementation=VECTOR_LOGLESS_CACHING keepRG=null justDetermineActiveRegions=false dontGenotype=false errorCorrectKmers=false debug=false debugGraphTransformations=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false allowCyclesInKmerGraphToGeneratePaths=false noFpga=false errorCorrectReads=false kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 pcr_indel_model=CONSERVATIVE activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
##GVCFBlock=minGQ=0(inclusive),maxGQ=5(exclusive)
##GVCFBlock=minGQ=20(inclusive),maxGQ=60(exclusive)
##GVCFBlock=minGQ=5(inclusive),maxGQ=20(exclusive)
##GVCFBlock=minGQ=60(inclusive),maxGQ=2147483647(exclusive)
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
##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=END,Number=1,Type=Integer,Description="Stop position of the interval">
##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=RAW_MQ,Number=1,Type=Float,Description="Raw data for RMS Mapping Quality">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
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##reference=file:///seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00141	HG01958	HG01530	NA12878
1	12141	.	C	<NON_REF>	.	.	END=12144	GT:DP:GQ:MIN_DP:PL	0:2:0:0:0,0	.	.	.
1	12145	.	C	<NON_REF>	.	.	END=12277	GT:DP:GQ:MIN_DP:PL	0:2:0:0:0,0	0/0:3:0:0:0,0,0	.	.
1	12278	.	C	<NON_REF>	.	.	END=12295	GT:DP:GQ:MIN_DP:PL	0:2:0:0:0,0	.	.	.
1	17384	.	TGG	T,TG,<NON_REF>	.	.	BaseQRankSum=1.07;ClippingRankSum=-1.067e+00;DP=9;MQ=55.72;MQ0=0;MQRankSum=0.056	GT:AD:DP:GQ:PL:SB	.	.	.	0/1/0:6,2,3,0:8:40:40,0,197,58,203,262,123,456,789,12,0,1,2,3,4,5,6,7,8,9:0,0,0,0
1	17385	.	G	A,T,*,<NON_REF>	.	.	BaseQRankSum=-2.074e+00;ClippingRankSum=-1.859e+00;DP=285;MQ=31.72;MQ0=3;MQRankSum=-4.320e-01;RAW_MQ=2.50;ReadPosRankSum=5.000e-03	GT:AD:DP:GQ:PGT:PID:PL:SB	0|1|0:58,22,17,17,17:80:99:0|1:17385_G_A:504,0,9807,678,1870,2548,123,456,789,12,1870,2548,123,456,789,12,456,789,12,12,1870,2548,123,456,789,12,456,789,12,12,456,789,12,12,12:58,0,22,0	2/2:0,37,120,37,37:120:99:0|1:17385_G_T:3336,4536,7349,358,958,0,4536,7349,958,7349,4536,7349,958,7349,7349:0,0,0,0	0/1:40,36,0,0,0:76:99:.:.:1018,0,1116,1137,1224,2361,1137,1224,2361,2361,1137,1224,2361,2361,2361:9,31,13,23	0/0/4:6,0,0,3,0:8:40:.:.:40,0,6,9,0,6,9,6,9,9,203,3,8,3,8,8,456,5,5,12,0,6,9,6,9,9,3,8,8,5,6,9,9,8,9:0,0,0,0
1	17386	.	G	*,<NON_REF>	.	.	DP=9	GT:AD:DP:GQ:PL:SB	.	.	.	0/0/2:6,3,0:8:40:40,203,456,12,0,3,5,6,8,9:0,0,0,0
