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=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another"> 10##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"> 11##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> 12##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> 13##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.7-43-gc7dbd4f,Date="Tue Jun 27 08:39:50 EDT 2017",Epoch=1498567190652,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/Users/gauthier/workspaces/gsa-unstable/private/gatk-tools-private/src/test/resources//NA12878.HiSeq.b37.chr20.10_11mb.bam] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[20:10433000-10437000, 20:10087820, 20:10684106] 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=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 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null use_jdk_deflater=false use_jdk_inflater=false 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 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[StrandBiasBySample] excludeAnnotation=[ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] group=[Standard, AS_Standard] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF bamOutput=null bamWriterType=CALLED_HAPLOTYPES emitDroppedReads=false disableOptimizations=false annotateNDA=false useNewAFCalculator=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 heterozygosity_stdev=0.01 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=6 max_genotype_count=1024 max_num_PL_values=100 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=FASTEST_AVAILABLE phredScaledGlobalReadMismappingRate=45 noFpga=false nativePairHmmThreads=1 useDoublePrecision=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 maxReadsInMemoryPerSample=30000 maxTotalReadsInMemory=10000000 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"> 14##GVCFBlock0-20=minGQ=0(inclusive),maxGQ=20(exclusive) 15##GVCFBlock20-100=minGQ=20(inclusive),maxGQ=100(exclusive) 16##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> 17##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> 18##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> 19##INFO=<ID=AS_BaseQRankSum,Number=A,Type=Float,Description="allele specific Z-score from Wilcoxon rank sum test of each Alt Vs. Ref base qualities"> 20##INFO=<ID=AS_FS,Number=A,Type=Float,Description="allele specific phred-scaled p-value using Fisher's exact test to detect strand bias of each alt allele"> 21##INFO=<ID=AS_InbreedingCoeff,Number=A,Type=Float,Description="Allele-specific inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation"> 22##INFO=<ID=AS_InbreedingCoeff,Number=A,Type=Float,Description="allele specific heterozygosity as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation; relate to inbreeding coefficient"> 23##INFO=<ID=AS_MQ,Number=A,Type=Float,Description="Allele-specific RMS Mapping Quality"> 24##INFO=<ID=AS_MQRankSum,Number=A,Type=Float,Description="Allele-specific Mapping Quality Rank Sum"> 25##INFO=<ID=AS_QD,Number=A,Type=Float,Description="Allele-specific Variant Confidence/Quality by Depth"> 26##INFO=<ID=AS_QUALapprox,Number=1,Type=String,Description="Allele-specific QUAL approximations"> 27##INFO=<ID=AS_RAW_BaseQRankSum,Number=1,Type=String,Description="raw data for allele specific rank sum test of base qualities"> 28##INFO=<ID=AS_RAW_MQ,Number=A,Type=Float,Description="Allele-specfic raw data for RMS Mapping Quality"> 29##INFO=<ID=AS_RAW_MQRankSum,Number=1,Type=String,Description="Allele-specific raw data for Mapping Quality Rank Sum"> 30##INFO=<ID=AS_RAW_ReadPosRankSum,Number=1,Type=String,Description="allele specific raw data for rank sum test of read position bias"> 31##INFO=<ID=AS_ReadPosRankSum,Number=A,Type=Float,Description="allele specific Z-score from Wilcoxon rank sum test of each Alt vs. Ref read position bias"> 32##INFO=<ID=AS_SB_TABLE,Number=1,Type=String,Description="Allele-specific forward/reverse read counts for strand bias tests"> 33##INFO=<ID=AS_SOR,Number=A,Type=Float,Description="Allele specific strand Odds Ratio of 2x|Alts| contingency table to detect allele specific strand bias"> 34##INFO=<ID=AS_VarDP,Number=1,Type=String,Description="Allele-specific (informative) depth over variant genotypes -- including ref, RAW format"> 35##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> 36##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> 37##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?"> 38##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval"> 39##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity"> 40##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> 41##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"> 42##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> 43##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"> 44##INFO=<ID=MQ_DP,Number=1,Type=Integer,Description="Depth over variant samples for better MQ calculation (deprecated -- use RAW_MQandDP instead.)"> 45##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth"> 46##INFO=<ID=QUALapprox,Number=1,Type=Integer,Description="Sum of PL[0] values; used to approximate the QUAL score"> 47##INFO=<ID=RAW_GT_COUNT,Number=3,Type=Integer,Description="Counts of genotypes w.r.t. the reference allele: 0/0, 0/*, */*, i.e. all alts lumped together; for use in calculating excess heterozygosity"> 48##INFO=<ID=RAW_MQ,Number=1,Type=Float,Description="Raw data for RMS Mapping Quality (deprecated -- use RAW_MQandDP instead.)"> 49##INFO=<ID=RAW_MQandDP,Number=2,Type=Integer,Description="Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated RAW_MQ formulation."> 50##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> 51##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias"> 52##INFO=<ID=VarDP,Number=1,Type=Integer,Description="(informative) depth over variant genotypes"> 53##contig=<ID=1,length=249250621> 54##contig=<ID=2,length=243199373> 55##contig=<ID=3,length=198022430> 56##contig=<ID=4,length=191154276> 57##contig=<ID=5,length=180915260> 58##contig=<ID=6,length=171115067> 59##contig=<ID=7,length=159138663> 60##contig=<ID=8,length=146364022> 61##contig=<ID=9,length=141213431> 62##contig=<ID=10,length=135534747> 63##contig=<ID=11,length=135006516> 64##contig=<ID=12,length=133851895> 65##contig=<ID=13,length=115169878> 66##contig=<ID=14,length=107349540> 67##contig=<ID=15,length=102531392> 68##contig=<ID=16,length=90354753> 69##contig=<ID=17,length=81195210> 70##contig=<ID=18,length=78077248> 71##contig=<ID=19,length=59128983> 72##contig=<ID=20,length=63025520> 73##contig=<ID=21,length=48129895> 74##contig=<ID=22,length=51304566> 75##contig=<ID=X,length=155270560> 76##contig=<ID=Y,length=59373566> 77##contig=<ID=MT,length=16569> 78##contig=<ID=GL000207.1,length=4262> 79##contig=<ID=GL000226.1,length=15008> 80##contig=<ID=GL000229.1,length=19913> 81##contig=<ID=GL000231.1,length=27386> 82##contig=<ID=GL000210.1,length=27682> 83##contig=<ID=GL000239.1,length=33824> 84##contig=<ID=GL000235.1,length=34474> 85##contig=<ID=GL000201.1,length=36148> 86##contig=<ID=GL000247.1,length=36422> 87##contig=<ID=GL000245.1,length=36651> 88##contig=<ID=GL000197.1,length=37175> 89##contig=<ID=GL000203.1,length=37498> 90##contig=<ID=GL000246.1,length=38154> 91##contig=<ID=GL000249.1,length=38502> 92##contig=<ID=GL000196.1,length=38914> 93##contig=<ID=GL000248.1,length=39786> 94##contig=<ID=GL000244.1,length=39929> 95##contig=<ID=GL000238.1,length=39939> 96##contig=<ID=GL000202.1,length=40103> 97##contig=<ID=GL000234.1,length=40531> 98##contig=<ID=GL000232.1,length=40652> 99##contig=<ID=GL000206.1,length=41001> 100##contig=<ID=GL000240.1,length=41933> 101##contig=<ID=GL000236.1,length=41934> 102##contig=<ID=GL000241.1,length=42152> 103##contig=<ID=GL000243.1,length=43341> 104##contig=<ID=GL000242.1,length=43523> 105##contig=<ID=GL000230.1,length=43691> 106##contig=<ID=GL000237.1,length=45867> 107##contig=<ID=GL000233.1,length=45941> 108##contig=<ID=GL000204.1,length=81310> 109##contig=<ID=GL000198.1,length=90085> 110##contig=<ID=GL000208.1,length=92689> 111##contig=<ID=GL000191.1,length=106433> 112##contig=<ID=GL000227.1,length=128374> 113##contig=<ID=GL000228.1,length=129120> 114##contig=<ID=GL000214.1,length=137718> 115##contig=<ID=GL000221.1,length=155397> 116##contig=<ID=GL000209.1,length=159169> 117##contig=<ID=GL000218.1,length=161147> 118##contig=<ID=GL000220.1,length=161802> 119##contig=<ID=GL000213.1,length=164239> 120##contig=<ID=GL000211.1,length=166566> 121##contig=<ID=GL000199.1,length=169874> 122##contig=<ID=GL000217.1,length=172149> 123##contig=<ID=GL000216.1,length=172294> 124##contig=<ID=GL000215.1,length=172545> 125##contig=<ID=GL000205.1,length=174588> 126##contig=<ID=GL000219.1,length=179198> 127##contig=<ID=GL000224.1,length=179693> 128##contig=<ID=GL000223.1,length=180455> 129##contig=<ID=GL000195.1,length=182896> 130##contig=<ID=GL000212.1,length=186858> 131##contig=<ID=GL000222.1,length=186861> 132##contig=<ID=GL000200.1,length=187035> 133##contig=<ID=GL000193.1,length=189789> 134##contig=<ID=GL000194.1,length=191469> 135##contig=<ID=GL000225.1,length=211173> 136##contig=<ID=GL000192.1,length=547496> 137##contig=<ID=NC_007605,length=171823> 138##reference=file:///seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta 139#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 14020 10087820 . C CAG,<NON_REF> 294.60 . AS_QUALapprox=|302|0;AS_RAW_BaseQRankSum=|-2.1,1|NaN;AS_RAW_MQ=123769.00|46800.00|0.00;AS_RAW_MQRankSum=|0.6,1|NaN;AS_RAW_ReadPosRankSum=|-0.4,1|NaN;AS_SB_TABLE=17,18|8,5|0,0;AS_VarDP=35|13|0;BaseQRankSum=-2.273;DP=93;MQRankSum=0.678;MQ_DP=93;QUALapprox=302;RAW_GT_COUNT=0,1,0;RAW_MQ=329810.00;RAW_MQandDP=329810,93;ReadPosRankSum=-0.492;VarDP=49 GT:AD:GQ:PL:SB 0/1:35,13,0:99:302,0,1079,483,1169,1922:17,18,9,5 14120 10433000 . G <NON_REF> . . END=10433307 GT:DP:GQ:MIN_DP:PL 0/0:36:21:29:0,21,315 14220 10433308 . G <NON_REF> . . END=10433311 GT:DP:GQ:MIN_DP:PL 0/0:27:6:27:0,6,90 14320 10433312 . C <NON_REF> . . END=10433319 GT:DP:GQ:MIN_DP:PL 0/0:16:75:16:0,75,839 14420 10433321 . A <NON_REF> . . END=10433321 GT:DP:GQ:MIN_DP:PL 0/0:29:33:29:0,33,495 14520 10433322 . A AT,<NON_REF> 116.60 . AS_QUALapprox=|124|0;AS_RAW_BaseQRankSum=|2.5,1|NaN;AS_RAW_MQ=14418.00|9723.00|0.00;AS_RAW_MQRankSum=|1.1,1|NaN;AS_RAW_ReadPosRankSum=|2.0,1|NaN;AS_SB_TABLE=5,6|2,3|0,0;AS_VarDP=11|5|0;BaseQRankSum=2.564;DP=35;MQRankSum=1.122;MQ_DP=35;QUALapprox=124;RAW_GT_COUNT=0,1,0;RAW_MQ=67710.00;RAW_MQandDP=67710,35;ReadPosRankSum=2.044;VarDP=16 GT:AD:GQ:PL:SB 0/1:11,5,0:99:124,0,369,158,384,542:5,6,2,3 14620 10433324 . A T,<NON_REF> 220.64 . AS_QUALapprox=|228|0;AS_RAW_BaseQRankSum=|2.2,1|NaN;AS_RAW_MQ=11895.00|10564.00|0.00;AS_RAW_MQRankSum=|0.5,1|NaN;AS_RAW_ReadPosRankSum=|1.5,1|NaN;AS_SB_TABLE=2,6|2,4|0,0;AS_VarDP=8|6|0;BaseQRankSum=2.279;DP=33;MQRankSum=0.584;MQ_DP=33;QUALapprox=228;RAW_GT_COUNT=0,1,0;RAW_MQ=60510.00;RAW_MQandDP=60510,33;ReadPosRankSum=1.543;VarDP=14 GT:AD:GQ:PGT:PID:PL:SB 0/1:8,6,0:99:0|1:10433324_A_T:228,0,275,252,294,546:2,6,2,4 14720 10433326 . A T,<NON_REF> 220.64 . AS_QUALapprox=|228|0;AS_RAW_BaseQRankSum=|0.8,1|NaN;AS_RAW_MQ=11895.00|10564.00|0.00;AS_RAW_MQRankSum=|0.5,1|NaN;AS_RAW_ReadPosRankSum=|1.4,1|NaN;AS_SB_TABLE=2,6|2,4|0,0;AS_VarDP=8|6|0;BaseQRankSum=0.874;DP=31;MQRankSum=0.584;MQ_DP=31;QUALapprox=228;RAW_GT_COUNT=0,1,0;RAW_MQ=53310.00;RAW_MQandDP=53310,31;ReadPosRankSum=1.403;VarDP=14 GT:AD:GQ:PGT:PID:PL:SB 0/1:8,6,0:99:0|1:10433324_A_T:228,0,275,252,293,546:2,6,2,4 14820 10433328 . A T,ATATAT,<NON_REF> 902.06 . AS_QUALapprox=|742|499|0;AS_RAW_BaseQRankSum=|||;AS_RAW_MQ=0.00|10564.00|2523.00|0.00;AS_RAW_MQRankSum=|||;AS_RAW_ReadPosRankSum=|||;AS_SB_TABLE=0,0|2,4|1,2|0,0;AS_VarDP=0|6|3|0;DP=30;MQ_DP=30;QUALapprox=919;RAW_GT_COUNT=0,0,1;RAW_MQ=49710.00;RAW_MQandDP=49710,30;VarDP=9 GT:AD:GQ:PL:SB 1/2:0,6,3,0:99:919,177,246,420,0,500,676,211,530,804:0,0,3,6 14920 10433330 . T <NON_REF> . . END=10433330 GT:DP:GQ:MIN_DP:PL 0/0:27:12:27:0,12,900 15020 10433331 . A <NON_REF> . . END=10433344 GT:DP:GQ:MIN_DP:PL 0/0:27:47:25:0,47,810 15120 10433346 . T <NON_REF> . . END=10433347 GT:DP:GQ:MIN_DP:PL 0/0:32:72:32:0,72,1080 15220 10433349 . A <NON_REF> . . END=10433381 GT:DP:GQ:MIN_DP:PL 0/0:27:45:26:0,45,915 15320 10433382 . T C,<NON_REF> 624.64 . AS_QUALapprox=|632|0;AS_RAW_BaseQRankSum=|-1.9,1|NaN;AS_RAW_MQ=40862.00|45723.00|0.00;AS_RAW_MQRankSum=|1.0,1|NaN;AS_RAW_ReadPosRankSum=|0.2,1|NaN;AS_SB_TABLE=10,5|11,4|0,0;AS_VarDP=15|15|0;BaseQRankSum=-1.821;DP=30;MQRankSum=1.033;MQ_DP=30;QUALapprox=632;RAW_GT_COUNT=0,1,0;RAW_MQ=86585.00;RAW_MQandDP=86585,30;ReadPosRankSum=0.249;VarDP=30 GT:AD:GQ:PGT:PID:PL:SB 0/1:15,15,0:99:0|1:10433382_T_C:632,0,601,680,652,1332:10,5,11,4 15420 10433383 . G <NON_REF> . . END=10433390 GT:DP:GQ:MIN_DP:PL 0/0:32:84:31:0,84,1260 15520 10433391 . T C,<NON_REF> 623.64 . AS_QUALapprox=|631|0;AS_RAW_BaseQRankSum=|-0.3,1|NaN;AS_RAW_MQ=51662.00|52082.00|0.00;AS_RAW_MQRankSum=|1.3,1|NaN;AS_RAW_ReadPosRankSum=|1.5,1|NaN;AS_SB_TABLE=14,4|13,3|0,0;AS_VarDP=18|16|0;BaseQRankSum=-0.284;DP=34;MQRankSum=1.329;MQ_DP=34;QUALapprox=631;RAW_GT_COUNT=0,1,0;RAW_MQ=103744.00;RAW_MQandDP=103744,34;ReadPosRankSum=1.536;VarDP=34 GT:AD:GQ:PGT:PID:PL:SB 0/1:18,16,0:99:0|1:10433382_T_C:631,0,673,685,724,1409:14,4,13,3 15620 10433392 . A <NON_REF> . . END=10433467 GT:DP:GQ:MIN_DP:PL 0/0:37:84:33:0,84,1110 15720 10433468 . T C,<NON_REF> 645.64 . AS_QUALapprox=|653|0;AS_RAW_BaseQRankSum=|-1.4,1|NaN;AS_RAW_MQ=63049.00|69241.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|1.4,1|NaN;AS_SB_TABLE=13,5|12,8|0,0;AS_VarDP=18|20|0;BaseQRankSum=-1.312;DP=38;MQRankSum=0.076;MQ_DP=38;QUALapprox=653;RAW_GT_COUNT=0,1,0;RAW_MQ=132290.00;RAW_MQandDP=132290,38;ReadPosRankSum=1.463;VarDP=38 GT:AD:GQ:PL:SB 0/1:18,20,0:99:653,0,572,707,633,1339:13,5,12,8 15820 10433469 . A <NON_REF> . . END=10433559 GT:DP:GQ:MIN_DP:PL 0/0:47:99:47:0,99,1410 15920 10433560 . C A,<NON_REF> 987.64 . AS_QUALapprox=|995|0;AS_RAW_BaseQRankSum=|3.4,1|NaN;AS_RAW_MQ=111600.00|87769.00|0.00;AS_RAW_MQRankSum=|-1.1,1|NaN;AS_RAW_ReadPosRankSum=|1.3,1|NaN;AS_SB_TABLE=30,1|22,3|0,0;AS_VarDP=31|25|0;BaseQRankSum=3.497;DP=56;MQRankSum=-1.078;MQ_DP=56;QUALapprox=995;RAW_GT_COUNT=0,1,0;RAW_MQ=199369.00;RAW_MQandDP=199369,56;ReadPosRankSum=1.376;VarDP=56 GT:AD:GQ:PGT:PID:PL:SB 0/1:31,25,0:99:0|1:10433560_C_A:995,0,3032,1092,3110,4202:30,1,22,3 16020 10433561 . G <NON_REF> . . END=10433574 GT:DP:GQ:MIN_DP:PL 0/0:61:99:61:0,120,1800 16120 10433575 . C T,<NON_REF> 1143.64 . AS_QUALapprox=|1151|0;AS_RAW_BaseQRankSum=|3.8,1|NaN;AS_RAW_MQ=119641.00|100251.00|0.00;AS_RAW_MQRankSum=|-1.2,1|NaN;AS_RAW_ReadPosRankSum=|0.8,1|NaN;AS_SB_TABLE=31,3|26,4|0,0;AS_VarDP=34|30|0;BaseQRankSum=3.811;DP=64;MQRankSum=-1.123;MQ_DP=64;QUALapprox=1151;RAW_GT_COUNT=0,1,0;RAW_MQ=219892.00;RAW_MQandDP=219892,64;ReadPosRankSum=0.830;VarDP=64 GT:AD:GQ:PGT:PID:PL:SB 0/1:34,30,0:99:0|1:10433560_C_A:1151,0,3385,1260,3476,4735:31,3,26,4 16220 10433576 . G <NON_REF> . . END=10433593 GT:DP:GQ:MIN_DP:PL 0/0:60:99:60:0,120,1800 16320 10433594 . C T,<NON_REF> 1105.64 . AS_QUALapprox=|1113|0;AS_RAW_BaseQRankSum=|4.8,1|NaN;AS_RAW_MQ=108841.00|85615.00|0.00;AS_RAW_MQRankSum=|-2.4,1|NaN;AS_RAW_ReadPosRankSum=|-0.6,1|NaN;AS_SB_TABLE=28,3|25,4|0,0;AS_VarDP=31|29|0;BaseQRankSum=4.816;DP=61;MQRankSum=-2.334;MQ_DP=61;QUALapprox=1113;RAW_GT_COUNT=0,1,0;RAW_MQ=195825.00;RAW_MQandDP=195825,61;ReadPosRankSum=-0.502;VarDP=60 GT:AD:GQ:PGT:PID:PL:SB 0/1:31,29,0:99:0|1:10433560_C_A:1113,0,3070,1206,3160,4366:28,3,25,4 16420 10433595 . T <NON_REF> . . END=10433808 GT:DP:GQ:MIN_DP:PL 0/0:44:93:39:0,93,1395 16520 10433809 . A G,<NON_REF> 1135.64 . 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AS_QUALapprox=|1475|0;AS_RAW_BaseQRankSum=|0.9,1|NaN;AS_RAW_MQ=108000.00|133784.00|0.00;AS_RAW_MQRankSum=|-2.5,1|NaN;AS_RAW_ReadPosRankSum=|-0.9,1|NaN;AS_SB_TABLE=15,15|23,20|0,0;AS_VarDP=30|43|0;BaseQRankSum=0.903;DP=74;MQRankSum=-2.473;MQ_DP=74;QUALapprox=1475;RAW_GT_COUNT=0,1,0;RAW_MQ=245384.00;RAW_MQandDP=245384,74;ReadPosRankSum=-0.891;VarDP=73 GT:AD:GQ:PL:SB 0/1:30,43,0:99:1475,0,936,1565,1066,2631:15,15,23,20 17720 10434178 . G <NON_REF> . . END=10434257 GT:DP:GQ:MIN_DP:PL 0/0:75:99:75:0,120,1800 17820 10434258 . G A,<NON_REF> 1235.64 . AS_QUALapprox=|1243|0;AS_RAW_BaseQRankSum=|3.0,1|NaN;AS_RAW_MQ=109369.00|106451.00|0.00;AS_RAW_MQRankSum=|-2.9,1|NaN;AS_RAW_ReadPosRankSum=|-0.2,1|NaN;AS_SB_TABLE=19,12|24,14|0,0;AS_VarDP=31|38|0;BaseQRankSum=3.063;DP=70;MQRankSum=-2.871;MQ_DP=70;QUALapprox=1243;RAW_GT_COUNT=0,1,0;RAW_MQ=219420.00;RAW_MQandDP=219420,70;ReadPosRankSum=-0.155;VarDP=69 GT:AD:GQ:PL:SB 0/1:31,38,0:99:1243,0,1003,1337,1118,2455:19,12,24,14 17920 10434259 . 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AS_QUALapprox=|984|278|0;AS_RAW_BaseQRankSum=|||;AS_RAW_MQ=3600.00|25702.00|19682.00|0.00;AS_RAW_MQRankSum=|||;AS_RAW_ReadPosRankSum=|||;AS_SB_TABLE=1,0|14,10|4,3|0,0;AS_VarDP=1|24|7|0;BaseQRankSum=-1.450;DP=75;MQRankSum=-1.660;MQ_DP=75;QUALapprox=1225;RAW_GT_COUNT=0,0,1;RAW_MQ=201025.00;RAW_MQandDP=201025,75;ReadPosRankSum=1.303;VarDP=32 GT:AD:GQ:PL:SB 1/2:1,24,7,0:99:1225,241,589,947,0,970,1258,491,1017,1480:1,0,18,13 18920 10436249 . T <NON_REF> . . END=10436254 GT:DP:GQ:MIN_DP:PL 0/0:44:78:43:0,78,1170 19020 10436259 . A <NON_REF> . . END=10436259 GT:DP:GQ:MIN_DP:PL 0/0:42:90:42:0,90,1350 19120 10436261 . T <NON_REF> . . END=10436262 GT:DP:GQ:MIN_DP:PL 0/0:41:6:41:0,6,1320 19220 10436263 . A <NON_REF> . . END=10436414 GT:DP:GQ:MIN_DP:PL 0/0:39:68:38:0,68,1335 19320 10436415 . A G,<NON_REF> 1190.64 . AS_QUALapprox=|1198|0;AS_RAW_BaseQRankSum=|-2.8,1|NaN;AS_RAW_MQ=81904.00|141241.00|0.00;AS_RAW_MQRankSum=|0.4,1|NaN;AS_RAW_ReadPosRankSum=|-0.1,1|NaN;AS_SB_TABLE=15,8|17,23|0,0;AS_VarDP=23|40|0;BaseQRankSum=-2.775;DP=63;MQRankSum=0.399;MQ_DP=63;QUALapprox=1198;RAW_GT_COUNT=0,1,0;RAW_MQ=223145.00;RAW_MQandDP=223145,63;ReadPosRankSum=-0.063;VarDP=63 GT:AD:GQ:PL:SB 0/1:23,40,0:99:1198,0,691,1267,810,2077:15,8,17,23 19420 10436416 . C <NON_REF> . . END=10436581 GT:DP:GQ:MIN_DP:PL 0/0:65:99:65:0,120,1800 19520 10436582 . A G,<NON_REF> 1187.64 . AS_QUALapprox=|1195|0;AS_RAW_BaseQRankSum=|-1.4,1|NaN;AS_RAW_MQ=117410.00|103379.00|0.00;AS_RAW_MQRankSum=|-2.7,1|NaN;AS_RAW_ReadPosRankSum=|0.2,1|NaN;AS_SB_TABLE=16,18|21,16|0,0;AS_VarDP=34|37|0;BaseQRankSum=-1.326;DP=71;MQRankSum=-2.639;MQ_DP=71;QUALapprox=1195;RAW_GT_COUNT=0,1,0;RAW_MQ=220789.00;RAW_MQandDP=220789,71;ReadPosRankSum=0.267;VarDP=71 GT:AD:GQ:PL:SB 0/1:34,37,0:99:1195,0,1113,1298,1225,2522:16,18,21,16 19620 10436583 . T <NON_REF> . . END=10436699 GT:DP:GQ:MIN_DP:PL 0/0:87:99:87:0,120,1800 19720 10436700 . A G,<NON_REF> 1333.64 . AS_QUALapprox=|1341|0;AS_RAW_BaseQRankSum=|-1.4,1|NaN;AS_RAW_MQ=108000.00|141769.00|0.00;AS_RAW_MQRankSum=|-0.9,1|NaN;AS_RAW_ReadPosRankSum=|0.5,1|NaN;AS_SB_TABLE=18,12|21,19|0,0;AS_VarDP=30|40|0;BaseQRankSum=-1.329;DP=70;MQRankSum=-0.837;MQ_DP=70;QUALapprox=1341;RAW_GT_COUNT=0,1,0;RAW_MQ=249769.00;RAW_MQandDP=249769,70;ReadPosRankSum=0.581;VarDP=70 GT:AD:GQ:PL:SB 0/1:30,40,0:99:1341,0,961,1431,1081,2513:18,12,21,19 19820 10436701 . T <NON_REF> . . END=10436907 GT:DP:GQ:MIN_DP:PL 0/0:74:99:74:0,120,1800 19920 10436908 . C G,<NON_REF> 1361.64 . AS_QUALapprox=|1369|0;AS_RAW_BaseQRankSum=|-0.9,1|NaN;AS_RAW_MQ=145849.00|145638.00|0.00;AS_RAW_MQRankSum=|-1.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.2,1|NaN;AS_SB_TABLE=15,26|11,31|0,0;AS_VarDP=41|42|0;BaseQRankSum=-0.844;DP=83;MQRankSum=-0.994;MQ_DP=83;QUALapprox=1369;RAW_GT_COUNT=0,1,0;RAW_MQ=291487.00;RAW_MQandDP=291487,83;ReadPosRankSum=-0.148;VarDP=83 GT:AD:GQ:PL:SB 0/1:41,42,0:99:1369,0,1378,1492,1504,2996:15,26,11,31 20020 10436909 . A <NON_REF> . . END=10437000 GT:DP:GQ:MIN_DP:PL 0/0:79:99:79:0,120,1800 20120 10684106 . C <NON_REF> . . END=10684118 GT:DP:GQ:MIN_DP:PL 0/0:29:99:29:0,112,2450 202