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">
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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	.	AS_QUALapprox=|1143|0;AS_RAW_BaseQRankSum=|1.4,1|NaN;AS_RAW_MQ=115200.00|122400.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.5,1|NaN;AS_SB_TABLE=13,19|12,22|0,0;AS_VarDP=32|34|0;BaseQRankSum=1.405;DP=68;MQRankSum=0.000;MQ_DP=68;QUALapprox=1143;RAW_GT_COUNT=0,1,0;RAW_MQ=242569.00;RAW_MQandDP=242569,68;ReadPosRankSum=-0.445;VarDP=66	GT:AD:GQ:PL:SB	0/1:32,34,0:99:1143,0,1041,1240,1143,2383:13,19,12,22
16620	10433810	.	C	<NON_REF>	.	.	END=10433954	GT:DP:GQ:MIN_DP:PL	0/0:52:59:51:0,59,1305
16720	10433955	.	C	CGTGTGTGTGTAT,<NON_REF>	1027.60	.	AS_QUALapprox=|1035|0;AS_RAW_BaseQRankSum=|0.4,1|NaN;AS_RAW_MQ=59810.00|39497.00|0.00;AS_RAW_MQRankSum=|-4.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.8,1|NaN;AS_SB_TABLE=12,6|16,8|0,0;AS_VarDP=18|24|0;BaseQRankSum=0.422;DP=47;MQRankSum=-4.001;MQ_DP=47;QUALapprox=1035;RAW_GT_COUNT=0,1,0;RAW_MQ=117307.00;RAW_MQandDP=117307,47;ReadPosRankSum=-0.789;VarDP=42	GT:AD:GQ:PL:SB	0/1:18,24,0:99:1035,0,1217,1090,1298,2389:12,6,16,8
16820	10433957	.	T	<NON_REF>	.	.	END=10433965	GT:DP:GQ:MIN_DP:PL	0/0:51:60:51:0,60,900
16920	10433967	.	T	<NON_REF>	.	.	END=10433981	GT:DP:GQ:MIN_DP:PL	0/0:45:60:42:0,60,900
17020	10433985	.	T	<NON_REF>	.	.	END=10433985	GT:DP:GQ:MIN_DP:PL	0/0:38:75:38:0,75,1125
17120	10433987	.	T	<NON_REF>	.	.	END=10433987	GT:DP:GQ:MIN_DP:PL	0/0:37:78:37:0,78,1170
17220	10433991	.	T	<NON_REF>	.	.	END=10433992	GT:DP:GQ:MIN_DP:PL	0/0:36:72:36:0,72,1080
17320	10433994	.	A	<NON_REF>	.	.	END=10433994	GT:DP:GQ:MIN_DP:PL	0/0:32:75:32:0,75,1125
17420	10433995	.	C	<NON_REF>	.	.	END=10433995	GT:DP:GQ:MIN_DP:PL	0/0:31:18:31:0,18,855
17520	10433996	.	G	<NON_REF>	.	.	END=10434176	GT:DP:GQ:MIN_DP:PL	0/0:32:49:29:0,49,863
17620	10434177	.	A	T,<NON_REF>	1467.64	.	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	.	T	<NON_REF>	.	.	END=10434383	GT:DP:GQ:MIN_DP:PL	0/0:66:99:66:0,108,1620
18020	10434384	.	TA	T,<NON_REF>	782.60	.	AS_QUALapprox=|790|0;AS_RAW_BaseQRankSum=|-0.1,1|NaN;AS_RAW_MQ=123769.00|118800.00|0.00;AS_RAW_MQRankSum=|1.0,1|NaN;AS_RAW_ReadPosRankSum=|0.4,1|NaN;AS_SB_TABLE=22,13|21,12|0,0;AS_VarDP=35|33|0;BaseQRankSum=-0.100;DP=71;MQRankSum=1.000;MQ_DP=71;QUALapprox=790;RAW_GT_COUNT=0,1,0;RAW_MQ=253369.00;RAW_MQandDP=253369,71;ReadPosRankSum=0.497;VarDP=68	GT:AD:GQ:PL:SB	0/1:35,33,0:99:790,0,846,895,945,1840:22,13,21,12
18120	10434387	.	A	<NON_REF>	.	.	END=10434518	GT:DP:GQ:MIN_DP:PL	0/0:75:36:75:0,36,1800
18220	10434519	.	T	C,<NON_REF>	1464.64	.	AS_QUALapprox=|1472|0;AS_RAW_BaseQRankSum=|-3.2,1|NaN;AS_RAW_MQ=126000.00|154800.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.8,1|NaN;AS_SB_TABLE=18,17|19,24|0,0;AS_VarDP=35|43|0;BaseQRankSum=-3.137;DP=78;MQRankSum=0.000;MQ_DP=78;QUALapprox=1472;RAW_GT_COUNT=0,1,0;RAW_MQ=280800.00;RAW_MQandDP=280800,78;ReadPosRankSum=-0.749;VarDP=78	GT:AD:GQ:PL:SB	0/1:35,43,0:99:1472,0,1192,1577,1321,2898:18,17,19,24
18320	10434520	.	T	<NON_REF>	.	.	END=10435066	GT:DP:GQ:MIN_DP:PL	0/0:69:72:67:0,72,1080
18420	10435067	.	GTA	G,<NON_REF>	1446.60	.	AS_QUALapprox=|1454|0;AS_RAW_BaseQRankSum=|2.6,1|NaN;AS_RAW_MQ=108000.00|133200.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.2,1|NaN;AS_SB_TABLE=15,15|22,15|0,0;AS_VarDP=30|37|0;BaseQRankSum=2.601;DP=67;MQRankSum=0.000;MQ_DP=67;QUALapprox=1454;RAW_GT_COUNT=0,1,0;RAW_MQ=241200.00;RAW_MQandDP=241200,67;ReadPosRankSum=-0.183;VarDP=67	GT:AD:GQ:PL:SB	0/1:30,37,0:99:1454,0,1191,1544,1303,2847:15,15,22,15
18520	10435071	.	T	<NON_REF>	.	.	END=10435947	GT:DP:GQ:MIN_DP:PL	0/0:74:91:66:0,91,1800
18620	10435948	.	A	C,<NON_REF>	1137.64	.	AS_QUALapprox=|1145|0;AS_RAW_BaseQRankSum=|-4.7,1|NaN;AS_RAW_MQ=144000.00|107528.00|0.00;AS_RAW_MQRankSum=|-3.2,1|NaN;AS_RAW_ReadPosRankSum=|-1.6,1|NaN;AS_SB_TABLE=19,21|20,16|0,0;AS_VarDP=40|36|0;BaseQRankSum=-4.692;DP=76;MQRankSum=-3.121;MQ_DP=76;QUALapprox=1145;RAW_GT_COUNT=0,1,0;RAW_MQ=251528.00;RAW_MQandDP=251528,76;ReadPosRankSum=-1.594;VarDP=76	GT:AD:GQ:PL:SB	0/1:40,36,0:99:1145,0,1413,1266,1521,2787:19,21,20,16
18720	10435949	.	A	<NON_REF>	.	.	END=10436226	GT:DP:GQ:MIN_DP:PL	0/0:68:99:68:0,120,1800
18820	10436227	.	TTTTATTTATTTATTTATTTA	T,TTTTATTTATTTATTTATTTATTTA,<NON_REF>	1208.02	.	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
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