##fileformat=VCFv4.2
##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
##FILTER=<ID=LowQual,Description="Low quality">
##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=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=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
##GATKCommandLine.GenotypeGVCFs=<ID=GenotypeGVCFs,Version=3.4-46-gbc02625,Date="Wed Sep 07 11:46:24 CEST 2016",Epoch=1473241584158,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=/PUBLIC_DATA/Tools/GATK/bundle/2.8/b37/reference.b37.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 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=16 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 logging_level=INFO log_to_file=null help=false version=false variant=[(RodBindingCollection [(RodBinding name=variant source=3-gvcf/Sample-P.gvcf.gz)]), (RodBindingCollection [(RodBinding name=variant2 source=3-gvcf/Sample-M.gvcf.gz)]), (RodBindingCollection [(RodBinding name=variant3 source=3-gvcf/Sample-E.gvcf.gz)])] out=/NGS/Various/jzoeifj/4-vcf/Sample.vcf.gz 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=[InbreedingCoeff, FisherStrand, QualByDepth, ChromosomeCounts, StrandOddsRatio] dbsnp=(RodBinding name=dbsnp source=/PUBLIC_DATA/Tools/GATK/bundle/2.8/b37/dbSNP.146.b37.vcf.gz) filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.4-46-gbc02625,Date="Tue Sep 06 23:04:59 CEST 2016",Epoch=1473195899363,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[2-bam/Sample-P.sorted.dedup.withRG.real.BQSR.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=[SureSelectClinicalResearchExome_Padded.b37.bed] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/PUBLIC_DATA/Tools/GATK/bundle/2.8/b37/reference.b37.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 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 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=16 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 out=/NGS/Various/jzoeifj/3-gvcf/Sample-P.gvcf.gz likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name=dbsnp source=/PUBLIC_DATA/Tools/GATK/bundle/2.8/b37/dbSNP.146.b37.vcf.gz) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[ClippingRankSumTest, DepthPerSampleHC, StrandBiasBySample] excludeAnnotation=[ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=BP_RESOLUTION bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false 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=2 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 gcpHMM=10 pair_hmm_implementation=VECTOR_LOGLESS_CACHING pair_hmm_sub_implementation=ENABLE_ALL always_load_vector_logless_PairHMM_lib=false phredScaledGlobalReadMismappingRate=45 noFpga=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 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 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=false keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
##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=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
##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=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=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">
##INFO=<ID=ReverseComplementedAlleles,Number=0,Type=Flag,Description="The REF and the ALT alleles have been reverse complemented in liftover since the mapping from the previous reference to the current one was on the negative strand.">
##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
##INFO=<ID=SwappedAlleles,Number=0,Type=Flag,Description="The REF and the ALT alleles have been swapped in liftover due to changes in the reference. It is possible that not all INFO annotations reflect this swap, and in the genotypes, only the GT, PL, and AD fields have been modified. You should check the TAGS_TO_REVERSE parameter that was used during the LiftOver to be sure.">
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#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Sample-E	Sample-M	Sample-P
chr11	66568070	rs200958879	A	C	67.13	PASS	AC=1;AF=0.167;AN=6;BaseQRankSum=-7.360e-01;ClippingRankSum=0.736;DB;DP=54;FS=0.000;MLEAC=1;MLEAF=0.167;MQ=60.00;MQRankSum=-7.360e-01;QD=11.19;ReadPosRankSum=-7.360e-01;SOR=1.179	GT:AD:DP:GQ:PGT:PID:PL	0/1:5,1:6:98:0|1:66335541_A_C:98,0,143	0/0:21,0:21:48:.:.:0,48,720	0/0:25,2:27:51:.:.:0,51,782
chr12	13571906	.	C	A	1085.13	PASS	AC=1;AF=0.167;AN=6;BaseQRankSum=-5.289e+00;ClippingRankSum=-1.900e-01;DP=177;FS=2.373;MLEAC=1;MLEAF=0.167;MQ=60.00;MQRankSum=0.316;QD=17.22;ReadPosRankSum=-1.468e+00;SOR=0.424	GT:AD:DP:GQ:PL	0/1:25,38:63:99:1116,0,818	0/0:39,0:39:90:0,90,1350	0/0:75,0:75:99:0,120,1800
chr2	97185492	.	GGA	G	51.61	PASS	AC=1;AF=0.167;AN=6;BaseQRankSum=3.25;ClippingRankSum=-7.700e-02;DP=286;FS=14.028;MLEAC=1;MLEAF=0.167;MQ=48.23;MQRankSum=-2.071e+00;QD=0.48;ReadPosRankSum=-3.237e+00;SOR=3.352	GT:AD:DP:GQ:PGT:PID:PL	0/1:98,9:107:77:0|1:97851229_GGA_G:77,0,4172	0/0:54,0:58:99:.:.:0,163,2417	0/0:118,0:118:99:.:.:0,120,1800
chr20	30393585	rs111331725	T	C	1410.13	PASS	AC=1;AF=0.167;AN=6;BaseQRankSum=3.92;ClippingRankSum=0.437;DB;DP=1474;FS=0.000;MLEAC=1;MLEAF=0.167;MQ=42.77;MQRankSum=5.79;QD=2.71;ReadPosRankSum=0.721;SOR=0.658	GT:AD:DP:GQ:PL	0/1:435,85:520:99:1441,0,16993	0/0:327,18:345:99:0,120,1800	0/0:580,28:608:99:0,120,1800
chr3	113805419	rs768704096	G	C	60.13	PASS	AC=1;AF=0.167;AN=6;BaseQRankSum=-3.693e+00;ClippingRankSum=-2.980e-01;DB;DP=220;FS=87.112;MLEAC=1;MLEAF=0.167;MQ=60.00;MQRankSum=0.312;QD=0.81;ReadPosRankSum=-5.000e+00;SOR=5.278	GT:AD:DP:GQ:PL	0/1:61,13:74:91:91,0,2064	0/0:49,6:55:34:0,34,1720	0/0:83,8:91:46:0,46,2908
chr4	106247229	rs370040550	T	G	44.17	PASS	AC=1;AF=0.167;AN=6;BaseQRankSum=-4.669e+00;ClippingRankSum=0.663;DB;DP=183;FS=140.097;MLEAC=1;MLEAF=0.167;MQ=60.00;MQRankSum=-8.000e-02;QD=0.51;ReadPosRankSum=0.362;SOR=6.592	GT:AD:DP:GQ:PL	0/1:60,26:86:75:75,0,1645	0/0:29,5:34:20:0,20,988	0/0:60,2:62:99:0,120,1800
chr6	17600872	rs201905369	G	A	166.13	PASS	AC=1;AF=0.167;AN=6;BaseQRankSum=3.49;ClippingRankSum=0.402;DB;DP=106;FS=2.382;MLEAC=1;MLEAF=0.167;MQ=59.63;MQRankSum=-4.020e-01;QD=3.19;ReadPosRankSum=-4.020e-01;SOR=1.524	GT:AD:DP:GQ:PGT:PID:PL	0/1:45,7:52:99:0|1:17601035_A_G:197,0,21023	0/0:16,0:16:48:.:.:0,48,613	0/0:38,0:38:99:.:.:0,99,1485
chr8	99832370	rs199704158	A	T	36.13	PASS	AC=1;AF=0.167;AN=6;BaseQRankSum=-5.950e-01;ClippingRankSum=0.845;DB;DP=81;FS=0.000;MLEAC=1;MLEAF=0.167;MQ=58.26;MQRankSum=-2.849e+00;QD=1.09;ReadPosRankSum=-9.710e-01;SOR=0.017	GT:AD:DP:GQ:PGT:PID:PL	0/1:30,3:33:67:0|1:100844594_TAG_T:67,0,1830	0/0:14,1:15:31:.:.:0,31,493	0/0:31,1:32:58:.:.:0,58,1100