1##fileformat=VCFv4.2 2##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location"> 3##FILTER=<ID=LowQual,Description="Low quality"> 4##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> 5##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> 6##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> 7##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 8##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block"> 9##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> 10##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)"> 11##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> 12##GATKCommandLine.GenotypeGVCFs=<ID=GenotypeGVCFs,Version=3.5-95-g77e7e24,Date="Wed Apr 20 12:53:21 EDT 2016",Epoch=1461171201850,CommandLineOptions="analysis_type=GenotypeGVCFs input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/humgen/gsa-hpprojects/GATK/bundle/current/b37/human_g1k_v37_decoy.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false 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=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false 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=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 logging_level=INFO log_to_file=null help=false version=false variant=[(RodBindingCollection [(RodBinding name=variant source=./private/gatk-tools-private/src/test/resources/haploid-gvcf-1.vcf)]), (RodBindingCollection [(RodBinding name=variant2 source=./private/gatk-tools-private/src/test/resources/haploid-gvcf-2.vcf)])] out=/home/unix/rlevine/gsa-unstable/output12.vcf includeNonVariantSites=false uniquifySamples=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=2 annotation=[] group=[StandardAnnotation] dbsnp=(RodBinding name= source=UNBOUND) filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"> 13##GATKCommandLine=<ID=HaplotypeCaller,Version=3.2-75-g6a47c26,Date="Mon Aug 25 19:29:02 EDT 2014",Epoch=1409009342933,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/humgen/1kg/DCC/ftp/data/HG01187/exome_alignment/HG01187.mapped.ILLUMINA.bwa.PUR.exome.20111114.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=[/humgen/gsa-hpprojects/dev/valentin/omniploidy/single-sample-pipeline/out-ploidy1-exome/.queue/scatterGather/RunMe-1-sg/temp_001_of_200/scatter.intervals] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/humgen/gsa-hpprojects/GATK/bundle/current/b37/human_g1k_v37_decoy.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 refactor_NDN_cigar_string=false 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=false 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] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=1 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingTails=false consensus=false GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 minPruning=2 gcpHMM=10 includeUmappedReads=false useAllelesTrigger=false phredScaledGlobalReadMismappingRate=45 maxNumHaplotypesInPopulation=128 mergeVariantsViaLD=false doNotRunPhysicalPhasing=true pair_hmm_implementation=VECTOR_LOGLESS_CACHING keepRG=null justDetermineActiveRegions=false dontGenotype=false errorCorrectKmers=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"> 14##GVCFBlock=minGQ=0(inclusive),maxGQ=1(exclusive) 15##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> 16##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> 17##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> 18##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> 19##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases"> 20##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> 21##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?"> 22##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval"> 23##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity"> 24##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> 25##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes"> 26##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"> 27##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"> 28##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"> 29##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> 30##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads"> 31##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"> 32##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth"> 33##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> 34##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias"> 35##contig=<ID=1,length=249250621> 36##contig=<ID=2,length=243199373> 37##contig=<ID=3,length=198022430> 38##contig=<ID=4,length=191154276> 39##contig=<ID=5,length=180915260> 40##contig=<ID=6,length=171115067> 41##contig=<ID=7,length=159138663> 42##contig=<ID=8,length=146364022> 43##contig=<ID=9,length=141213431> 44##contig=<ID=10,length=135534747> 45##contig=<ID=11,length=135006516> 46##contig=<ID=12,length=133851895> 47##contig=<ID=13,length=115169878> 48##contig=<ID=14,length=107349540> 49##contig=<ID=15,length=102531392> 50##contig=<ID=16,length=90354753> 51##contig=<ID=17,length=81195210> 52##contig=<ID=18,length=78077248> 53##contig=<ID=19,length=59128983> 54##contig=<ID=20,length=63025520> 55##contig=<ID=21,length=48129895> 56##contig=<ID=22,length=51304566> 57##contig=<ID=X,length=155270560> 58##contig=<ID=Y,length=59373566> 59##contig=<ID=MT,length=16569> 60##contig=<ID=GL000207.1,length=4262> 61##contig=<ID=GL000226.1,length=15008> 62##contig=<ID=GL000229.1,length=19913> 63##contig=<ID=GL000231.1,length=27386> 64##contig=<ID=GL000210.1,length=27682> 65##contig=<ID=GL000239.1,length=33824> 66##contig=<ID=GL000235.1,length=34474> 67##contig=<ID=GL000201.1,length=36148> 68##contig=<ID=GL000247.1,length=36422> 69##contig=<ID=GL000245.1,length=36651> 70##contig=<ID=GL000197.1,length=37175> 71##contig=<ID=GL000203.1,length=37498> 72##contig=<ID=GL000246.1,length=38154> 73##contig=<ID=GL000249.1,length=38502> 74##contig=<ID=GL000196.1,length=38914> 75##contig=<ID=GL000248.1,length=39786> 76##contig=<ID=GL000244.1,length=39929> 77##contig=<ID=GL000238.1,length=39939> 78##contig=<ID=GL000202.1,length=40103> 79##contig=<ID=GL000234.1,length=40531> 80##contig=<ID=GL000232.1,length=40652> 81##contig=<ID=GL000206.1,length=41001> 82##contig=<ID=GL000240.1,length=41933> 83##contig=<ID=GL000236.1,length=41934> 84##contig=<ID=GL000241.1,length=42152> 85##contig=<ID=GL000243.1,length=43341> 86##contig=<ID=GL000242.1,length=43523> 87##contig=<ID=GL000230.1,length=43691> 88##contig=<ID=GL000237.1,length=45867> 89##contig=<ID=GL000233.1,length=45941> 90##contig=<ID=GL000204.1,length=81310> 91##contig=<ID=GL000198.1,length=90085> 92##contig=<ID=GL000208.1,length=92689> 93##contig=<ID=GL000191.1,length=106433> 94##contig=<ID=GL000227.1,length=128374> 95##contig=<ID=GL000228.1,length=129120> 96##contig=<ID=GL000214.1,length=137718> 97##contig=<ID=GL000221.1,length=155397> 98##contig=<ID=GL000209.1,length=159169> 99##contig=<ID=GL000218.1,length=161147> 100##contig=<ID=GL000220.1,length=161802> 101##contig=<ID=GL000213.1,length=164239> 102##contig=<ID=GL000211.1,length=166566> 103##contig=<ID=GL000199.1,length=169874> 104##contig=<ID=GL000217.1,length=172149> 105##contig=<ID=GL000216.1,length=172294> 106##contig=<ID=GL000215.1,length=172545> 107##contig=<ID=GL000205.1,length=174588> 108##contig=<ID=GL000219.1,length=179198> 109##contig=<ID=GL000224.1,length=179693> 110##contig=<ID=GL000223.1,length=180455> 111##contig=<ID=GL000195.1,length=182896> 112##contig=<ID=GL000212.1,length=186858> 113##contig=<ID=GL000222.1,length=186861> 114##contig=<ID=GL000200.1,length=187035> 115##contig=<ID=GL000193.1,length=189789> 116##contig=<ID=GL000194.1,length=191469> 117##contig=<ID=GL000225.1,length=211173> 118##contig=<ID=GL000192.1,length=547496> 119##contig=<ID=NC_007605,length=171823> 120##contig=<ID=hs37d5,length=35477943> 121#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00610 122Y 4968655 . T G 408.77 . AC=1;AF=1.00;AN=1;DP=9;FS=0.000;MQ=28.47;MQ0=0;QD=24.05;SOR=1.061 GT:AD:DP:GQ:PL 1:0,9:9:99:223,0 123Y 6948831 . C T 780.76 . AC=1;AF=1.00;AN=1;DP=25;FS=0.000;MQ=46.20;MQ0=0;QD=31.23;SOR=1.358 GT:AD:DP:GQ:PL 1:0,25:25:99:812,0 124Y 14832620 . G . 1206.76 . AN=1;DP=13;FS=0.000;MQ=60.00;MQ0=0;QD=32.62;SOR=1.121 GT:AD:DP:PL 0:13:13:0 125