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tableToVCF.vcf
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tableToVCF.vcf
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##fileformat=VCFv4.2
##reference=file:///media/everestial007/SeagateBackup4.0TB/RNAseq_Data_Analyses/02_Alignment_To_Ref - New/GVCF_Calls_onGenes-RunningTest01/02-JointGenotyping_MySpF1/lyrata_genome.fa
##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
##FILTER=<ID=LowQual,Description="Low quality">
##FILTER=<ID=my_indel_filter,Description="QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0">
##FILTER=<ID=my_snp_filter,Description="QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0">
##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=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.CombineVariants=<ID=CombineVariants,CommandLineOptions="analysis_type=CombineVariants input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=lyrata_genome.fa 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 secondsBetweenProgressUpdates=10 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 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=[(RodBindingCollection [(RodBinding name=HignConfSNPs source=HighConf_Variants.asPASSED.AllSamples.vcf)]), (RodBindingCollection [(RodBinding name=SNPs source=DNA_Samples.Passed.SNPs_allHetsRemoved.vcf)]), (RodBindingCollection [(RodBinding name=InDels source=DNA_Samples.Passed.InDels_allHetsRemoved.vcf)])] out=/media/everestial007/SeagateBackup4.0TB/RNAseq_Data_Analyses/02_Alignment_To_Ref - New/GVCF_Calls_onGenes-RunningTest01/02-JointGenotyping_MySpF1/DNA_Samples.Passed_Variants.vcf genotypemergeoption=UNSORTED filteredrecordsmergetype=KEEP_IF_ANY_UNFILTERED multipleallelesmergetype=BY_TYPE rod_priority_list=null printComplexMerges=false filteredAreUncalled=false minimalVCF=false excludeNonVariants=false setKey=set assumeIdenticalSamples=false minimumN=1 suppressCommandLineHeader=false mergeInfoWithMaxAC=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false",Date="Thu Dec 21 23:56:42 EST 2017",Epoch=1513918602988,Version=3.7-0-gcfedb67>
##GATKCommandLine.GenotypeGVCFs=<ID=GenotypeGVCFs,CommandLineOptions="analysis_type=GenotypeGVCFs input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=lyrata_genome.fa 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 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 variant=[(RodBindingCollection [(RodBinding name=variant source=MA605.raw.snps.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant2 source=MA611.raw.snps.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant3 source=MA622.raw.snps.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant4 source=MA625.raw.snps.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant5 source=MA629.raw.snps.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant6 source=Ncm8.raw.snps.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant7 source=Sp3.raw.snps.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant8 source=Sp21.raw.snps.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant9 source=Sp76.raw.snps.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant10 source=Sp154.raw.snps.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant11 source=Sp164.raw.snps.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant12 source=SpNor33.raw.snps.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant13 source=ms01e.raw.snps.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant14 source=ms02g.raw.snps.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant15 source=ms03g.raw.snps.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant16 source=ms04h.raw.snps.indels.g.vcf)])] out=/media/everestial007/SeagateBackup4.0TB/RNAseq_Data_Analyses/02_Alignment_To_Ref - New/GVCF_Calls_onGenes/raw_variants.AllSamples.MySpF1.vcf includeNonVariantSites=false uniquifySamples=false annotateNDA=false useNewAFCalculator=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 heterozygosity_stdev=0.01 standard_min_confidence_threshold_for_calling=10.0 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 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",Date="Sat Dec 16 20:17:48 EST 2017",Epoch=1513473468011,Version=3.8-0-ge9d806836>
##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[good_Coverage.mapQ20.sorted.MA611.bam] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[2:15881000-15902000, 3:12165000-12174000] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/home/bkgiri/apps/RefGenomeN_index/lyrata_genome.fa 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=[StandardAnnotation, StandardHCAnnotation] 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",Date="Fri Dec 15 18:29:51 EST 2017",Epoch=1513380591593,Version=3.8-0-ge9d806836>
##GATKCommandLine.SelectVariants.2=<ID=SelectVariants,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=lyrata_genome.fa 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 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 variant=(RodBinding name=variant source=Remaining.Variants.AllSamples.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/media/everestial007/SeagateBackup4.0TB/RNAseq_Data_Analyses/02_Alignment_To_Ref - New/GVCF_Calls_onGenes-RunningTest01/02-JointGenotyping_MySpF1/DNA_Samples.raw_SNPs.vcf sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[ms01e, ms02g, ms03g, ms04h] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[vc.getCalledChrCount() == 0] invertselect=true excludeNonVariants=false excludeFiltered=false preserveAlleles=false removeUnusedAlternates=true restrictAllelesTo=ALL keepOriginalAC=false keepOriginalDP=false mendelianViolation=false invertMendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[SNP] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 maxNOCALLnumber=2147483647 maxNOCALLfraction=1.0 setFilteredGtToNocall=false ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false forceValidOutput=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false",Date="Thu Dec 21 23:18:22 EST 2017",Epoch=1513916302870,Version=3.8-0-ge9d806836>
##GATKCommandLine.SelectVariants.3=<ID=SelectVariants,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=lyrata_genome.fa 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 secondsBetweenProgressUpdates=10 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 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=DNA_Samples.Filtered_SNPs.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/media/everestial007/SeagateBackup4.0TB/RNAseq_Data_Analyses/02_Alignment_To_Ref - New/GVCF_Calls_onGenes-RunningTest01/02-JointGenotyping_MySpF1/DNA_Samples.Passed_SNPs.vcf sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[vc.isNotFiltered()] invertselect=false excludeNonVariants=false excludeFiltered=false preserveAlleles=false removeUnusedAlternates=false restrictAllelesTo=ALL keepOriginalAC=false keepOriginalDP=false mendelianViolation=false invertMendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 maxNOCALLnumber=2147483647 maxNOCALLfraction=1.0 setFilteredGtToNocall=false ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false forceValidOutput=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false",Date="Thu Dec 21 23:20:01 EST 2017",Epoch=1513916401173,Version=3.7-0-gcfedb67>
##GATKCommandLine.SelectVariants.4=<ID=SelectVariants,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=lyrata_genome.fa 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 secondsBetweenProgressUpdates=10 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 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=DNA_Samples.Passed_SNPs.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/media/everestial007/SeagateBackup4.0TB/RNAseq_Data_Analyses/02_Alignment_To_Ref - New/GVCF_Calls_onGenes-RunningTest01/02-JointGenotyping_MySpF1/DNA_Samples.Passed.SNPs_allHetsRemoved.vcf sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[vc.getHetCount() == vc.getCalledChrCount()/2] invertselect=true excludeNonVariants=false excludeFiltered=false preserveAlleles=false removeUnusedAlternates=false restrictAllelesTo=ALL keepOriginalAC=false keepOriginalDP=false mendelianViolation=false invertMendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 maxNOCALLnumber=2147483647 maxNOCALLfraction=1.0 setFilteredGtToNocall=false ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false forceValidOutput=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false",Date="Thu Dec 21 23:20:23 EST 2017",Epoch=1513916423031,Version=3.7-0-gcfedb67>
##GATKCommandLine.SelectVariants=<ID=SelectVariants,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=lyrata_genome.fa 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 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 variant=(RodBinding name=variant source=raw_variants.AllSamples.MySpF1.vcf) discordance=(RodBinding name=discordance source=Detlef.Variants.asPASSED.vcf) concordance=(RodBinding name= source=UNBOUND) out=/media/everestial007/SeagateBackup4.0TB/RNAseq_Data_Analyses/02_Alignment_To_Ref - New/GVCF_Calls_onGenes-RunningTest01/02-JointGenotyping_MySpF1/Remaining.Variants.AllSamples.vcf sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[] invertselect=false excludeNonVariants=false excludeFiltered=false preserveAlleles=false removeUnusedAlternates=false restrictAllelesTo=ALL keepOriginalAC=false keepOriginalDP=false mendelianViolation=false invertMendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 maxNOCALLnumber=2147483647 maxNOCALLfraction=1.0 setFilteredGtToNocall=false ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false forceValidOutput=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false",Date="Thu Dec 21 23:10:31 EST 2017",Epoch=1513915831133,Version=3.8-0-ge9d806836>
##GATKCommandLine.VariantFiltration=<ID=VariantFiltration,CommandLineOptions="analysis_type=VariantFiltration input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=lyrata_genome.fa 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 secondsBetweenProgressUpdates=10 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 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=DNA_Samples.raw_SNPs.vcf) mask=(RodBinding name= source=UNBOUND) out=/media/everestial007/SeagateBackup4.0TB/RNAseq_Data_Analyses/02_Alignment_To_Ref - New/GVCF_Calls_onGenes-RunningTest01/02-JointGenotyping_MySpF1/DNA_Samples.Filtered_SNPs.vcf filterExpression=[QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0] filterName=[my_snp_filter] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskExtension=0 maskName=Mask filterNotInMask=false missingValuesInExpressionsShouldEvaluateAsFailing=false invalidatePreviousFilters=false invertFilterExpression=false invertGenotypeFilterExpression=false setFilteredGtToNocall=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false",Date="Thu Dec 21 23:19:58 EST 2017",Epoch=1513916398266,Version=3.7-0-gcfedb67>
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##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">
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2 15881436 . GA G . PASS AF=0.042;AN=6;BaseQRankSum=2.00;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:.:12:0,12,157 .:.:.:.
2 15881445 . A C . PASS AF=0.038;AN=8;BaseQRankSum=1.45;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:.:15:0,15,210 ./.:.:.:.,.,.
2 15881550 . C T . PASS AF=0.125;AN=14;BaseQRankSum=0.264;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:.:39:0,39,585 0/0:.:99:0,102,1800
2 15881551 . A T . PASS AF=0.125;AN=14;BaseQRankSum=0.339;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:.:39:0,39,585 0/0:.:99:0,102,1800
2 15881553 . C A . PASS AF=0.125;AN=14;BaseQRankSum=-3.600e-01;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:.:33:0,33,495 0/1:4:99:787,0,1002
2 15881764 . T C . PASS AF=0.250;AN=14;BaseQRankSum=-8.290e-01;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:.:48:0,48,600 0/1:4:99:2626,0,1270
2 15881767 . C T . PASS AF=0.125;AN=14;BaseQRankSum=-1.792e+00;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:.:48:.,.,. 0/0:4:99:0,120,1800
2 15881810 . A C . PASS AF=1.00;AN=14;BaseQRankSum=.;ClippingRankSum=. GT:PI:GQ:PL 1/1:.:54:669,54,0 1/1:4:99:5029,403,0
2 15881944 . C T . PASS AF=0.375;AN=14;BaseQRankSum=-7.080e-01;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:.:42:0,42,505 0/1:4:99:2001,0,1480
2 15881974 . C A . PASS AF=0.375;AN=14;BaseQRankSum=-2.780e-01;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:.:36:0,36,540 0/1:4:99:1503,0,1430
2 15881989 . C A . PASS AF=0.125;AN=14;BaseQRankSum=0.771;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:.:33:.,.,. 0/0:4:99:0,120,1800
2 15882091 . A T . PASS AF=0.375;AN=14;BaseQRankSum=0.116;ClippingRankSum=0.00 GT:PI:GQ:PL 1/1:.:21:244,21,0 0/1:4:99:1098,0,991
2 15882148 . T G . PASS AF=0.125;AN=14;BaseQRankSum=-5.290e-01;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:.:39:0,39,474 0/0:4:99:0,120,1800
2 15882328 . T A . PASS AF=0.125;AN=14;BaseQRankSum=0.712;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:.:21:0,21,315 0/1:4:99:1814,0,1080
2 15882364 . T G . PASS AF=0.125;AN=14;BaseQRankSum=0.669;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:.:27:0,27,325 0/1:4:99:2203,0,1080
2 15882451 . T C . PASS AF=0.250;AN=14;BaseQRankSum=0.652;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:.:9:0,9,135 0/1:4:99:3896,0,1601
2 15882454 . T C . PASS AF=0.250;AN=14;BaseQRankSum=0.769;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:.:6:0,6,90 0/1:4:99:4138,0,1708
2 15882493 . T C . PASS AF=0.250;AN=14;BaseQRankSum=0.301;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:.:21:0,21,202 0/1:4:99:3847,0,2156
2 15882505 . T A . PASS AF=0.250;AN=14;BaseQRankSum=-1.241e+00;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:.:18:0,18,270 0/1:4:99:3795,0,2137
2 15882583 . G T . PASS AF=0.125;AN=14;BaseQRankSum=-3.450e-01;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:.:27:0,27,307 0/0:4:99:0,120,1800
2 15882592 . G A . PASS AF=0.500;AN=14;BaseQRankSum=0.148;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:.:33:0,33,368 0/1:4:99:3661,0,3127
2 15882601 . C T . PASS AF=0.125;AN=14;BaseQRankSum=-3.060e-01;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:.:33:.,.,. 0/0:4:99:0,120,1800
2 15882607 . C T . PASS AF=0.125;AN=14;BaseQRankSum=-4.490e-01;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:.:30:0,30,307 0/1:4:99:3611,0,3078
2 15882615 . A G . PASS AF=0.500;AN=14;BaseQRankSum=1.55;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:.:24:0,24,360 0/1:4:99:3480,0,3075
2 15882618 . G C . PASS AF=0.500;AN=14;BaseQRankSum=-4.170e-01;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:.:24:0,24,360 0/1:4:99:3475,0,3052
2 15882712 . C T . PASS AF=0.250;AN=14;BaseQRankSum=0.393;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:.:12:0,12,156 0/0:4:99:0,120,1800
2 15882736 . T G . PASS AF=0.250;AN=14;BaseQRankSum=-2.120e-01;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:.:24:0,24,254 0/0:4:99:0,120,1800
2 15882770 . G A . PASS AF=0.250;AN=14;BaseQRankSum=-9.610e-01;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:.:30:0,30,376 0/0:4:99:0,120,1800
2 15882812 . C A . PASS AF=0.125;AN=14;BaseQRankSum=-1.440e+00;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:.:45:0,45,675 0/0:4:99:0,120,1800
2 15882822 . G A . PASS AF=0.500;AN=12;BaseQRankSum=1.05;ClippingRankSum=0.00 GT:PI:GQ:PL 0/1:2:99:165,0,300 0/1:4:99:2471,0,3565
2 15882922 . A T . PASS AF=0.083;AN=10;BaseQRankSum=1.69;ClippingRankSum=0.00 GT:PI:GQ:PL 0/1:2:99:219,0,221 ./.:.:.:.,.,.
2 15882938 . C T . PASS AF=0.500;AN=10;BaseQRankSum=-6.000e-03;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:2:45:0,45,675 ./.:.:.:0,0,0
2 15882952 . A G . PASS AF=0.500;AN=10;BaseQRankSum=1.75;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:2:45:0,45,675 ./.:.:.:0,0,0
2 15882967 . T C . PASS AF=1.00;AN=8;BaseQRankSum=1.40;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:2:54:0,54,810 ./.:.:.:0,0,0
2 15882973 . A G . PASS AF=1.00;AN=8;BaseQRankSum=1.48;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:2:51:0,51,765 ./.:.:.:0,0,0
2 15883029 . T C . PASS AF=0.375;AN=14;BaseQRankSum=0.555;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:2:30:0,30,396 0/0:4:99:0,120,1800
2 15883059 . C G . PASS AF=0.500;AN=14;BaseQRankSum=0.088;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:2:15:0,15,225 0/1:4:99:4138,0,1973
2 15883065 . C T . PASS AF=0.375;AN=14;BaseQRankSum=1.31;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:2:18:0,18,210 0/0:4:99:0,120,1800
2 15883070 . G C . PASS AF=0.125;AN=14;BaseQRankSum=-8.410e-01;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:2:21:0,21,242 0/1:4:99:6258,0,3613
2 15883071 . T C . PASS AF=0.500;AN=14;BaseQRankSum=3.06;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:2:21:0,21,242 0/1:4:99:6258,0,3613
2 15883083 . G A . PASS AF=0.375;AN=14;BaseQRankSum=1.21;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:2:21:0,21,242 0/0:4:99:0,105,1575
2 15883230 . A T . PASS AF=0.167;AN=12;BaseQRankSum=1.65;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:2:27:0,27,362 0/0:4:6:0,6,81
2 15883328 . T A . PASS AF=0.333;AN=6;BaseQRankSum=.;ClippingRankSum=. GT:PI:GQ:PL .:.:.:. 0/0:4:21:0,21,184
2 15883333 . G A . PASS AF=0.167;AN=12;BaseQRankSum=0.611;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:2:33:0,33,448 0/1:.:28:28,0,123
2 15883371 . A T . PASS AF=0.083;AN=14;BaseQRankSum=-3.420e-01;ClippingRankSum=0.00 GT:PI:GQ:PL 0/1:4:85:150,0,85 0/0:4:18:.,.,.
2 15883431 . A T . PASS AF=0.250;AN=14;BaseQRankSum=2.56;ClippingRankSum=0.00 GT:PI:GQ:PL 0/1:4:99:151,0,111 0/1:4:99:3743,0,3352
2 15883479 . C CCTTTT . PASS AF=0.036;AN=10;BaseQRankSum=-8.510e-01;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:24:0,24,275 ./.:.:.:.,.,.
2 15883529 . C T . PASS AF=0.500;AN=8;BaseQRankSum=1.20;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:30:0,30,422 ./.:.:.:0,0,0
2 15883590 . TA T . PASS AF=0.393;AN=10;BaseQRankSum=1.53;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:21:0,21,315 0/0:4:3:.,.,.
2 15883606 . C T . PASS AF=0.033;AN=12;BaseQRankSum=-2.157e+00;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:15:0,15,225 0/0:4:18:.,.,.
2 15883644 . C CT . PASS AF=0.125;AN=14;BaseQRankSum=0.00;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:15:0,15,225 0/0:4:36:0,36,540
2 15883661 . T A . PASS AF=0.042;AN=14;BaseQRankSum=-2.093e+00;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:6:0,6,90 0/0:4:0:.,.,.
2 15883674 . G C . PASS AF=0.250;AN=14;BaseQRankSum=0.00;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:12:0,12,117 0/0:4:36:0,36,415
2 15883678 . C CA . PASS AF=0.250;AN=8;BaseQRankSum=-5.240e-01;ClippingRankSum=0.00 GT:PI:GQ:PL .:.:.:. 0/0:4:36:0,36,415
2 15883728 . C T . PASS AF=0.125;AN=14;BaseQRankSum=-5.240e-01;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:15:0,15,193 0/0:4:27:0,27,405
2 15883764 . A . . PASS AF=.;AN=4;BaseQRankSum=.;ClippingRankSum=. GT:PI:GQ:PL .:.:.:. ./.:.:.:.
2 15883765 . GTA G . PASS AF=0.250;AN=14;BaseQRankSum=1.50;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:9:0,9,135 0/0:4:3:0,3,45
2 15883769 . T A . PASS AF=0.333;AN=12;BaseQRankSum=1.50;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:9:0,9,135 0/0:4:3:0,3,45
2 15883771 . A C . PASS AF=0.333;AN=12;BaseQRankSum=1.38;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:9:0,9,135 0/0:4:3:0,3,45
2 15883782 . T A . PASS AF=0.357;AN=10;BaseQRankSum=1.38;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:9:0,9,93 ./.:.:.:.,.,.
2 15883783 . C A . PASS AF=0.357;AN=10;BaseQRankSum=1.38;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:9:0,9,93 ./.:.:.:.,.,.
2 15883785 . T TA . PASS AF=0.357;AN=10;BaseQRankSum=1.02;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:9:0,9,93 ./.:.:.:.,.,.
2 15883792 . A AAT . PASS AF=0.385;AN=8;BaseQRankSum=1.15;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:9:0,9,93 ./.:.:.:.,.,.
2 15883804 . T C . PASS AF=0.393;AN=10;BaseQRankSum=-4.310e-01;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:9:0,9,91 0/0:4:3:.,.,.
2 15883806 . G T . PASS AF=0.462;AN=8;BaseQRankSum=.;ClippingRankSum=. GT:PI:GQ:PL 0/0:4:9:0,9,91 ./.:.:.:.,.,.
2 15883861 . A G . PASS AF=0.033;AN=12;BaseQRankSum=1.38;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:15:0,15,225 0/0:4:3:.,.,.
2 15883862 . G T . PASS AF=0.033;AN=12;BaseQRankSum=1.98;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:15:0,15,225 0/0:4:3:.,.,.
2 15883889 . T C . PASS AF=0.167;AN=12;BaseQRankSum=1.02;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:15:0,15,191 0/0:4:3:0,3,39
2 15883894 . T G . PASS AF=0.167;AN=12;BaseQRankSum=1.08;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:15:0,15,184 0/0:4:3:0,3,39
2 15883904 . A G . PASS AF=0.033;AN=12;BaseQRankSum=1.62;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:15:0,15,184 0/0:4:3:.,.,.
2 15883912 . G T . PASS AF=0.033;AN=12;BaseQRankSum=-1.800e-01;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:18:0,18,181 0/0:4:6:.,.,.
2 15883930 . A AATG . PASS AF=0.033;AN=12;BaseQRankSum=0.366;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:0:0,0,108 0/0:4:9:.,.,.
2 15883933 . G T . PASS AF=0.313;AN=14;BaseQRankSum=0.792;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:18:0,18,171 0/0:4:0:.,.,.
2 15883936 . G A . PASS AF=0.125;AN=14;BaseQRankSum=1.61;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:18:0,18,171 0/0:4:0:0,0,42
2 15883953 . G C . PASS AF=0.136;AN=12;BaseQRankSum=0.900;ClippingRankSum=0.00 GT:PI:GQ:PL ./.:.:.:0,0,0 0/0:4:15:.,.,.
2 15883965 . C G . PASS AF=0.500;AN=14;BaseQRankSum=-6.300e-02;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:15:0,15,166 0/1:7:75:75,0,120
2 15883979 . A T . PASS AF=1.00;AN=14;BaseQRankSum=.;ClippingRankSum=. GT:PI:GQ:PL 1/1:4:15:178,15,0 1/1:7:15:184,15,0
2 15883987 . T C . PASS AF=0.500;AN=14;BaseQRankSum=-5.240e-01;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:9:0,9,135 0/1:7:75:75,0,120
2 15883998 . A G . PASS AF=0.500;AN=14;BaseQRankSum=-4.260e-01;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:9:0,9,135 0/1:7:75:75,0,120
2 15884017 . A T . PASS AF=0.375;AN=14;BaseQRankSum=0.842;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:15:0,15,212 0/0:7:0:0,0,51
2 15884047 . A T . PASS AF=0.500;AN=10;BaseQRankSum=1.09;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:15:0,15,198 ./.:.:.:0,0,0
2 15884078 . G GC,GCC . PASS AF=0.667;AN=12;BaseQRankSum=0.070;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:6:0,6,90,6,90,90 ./.:.:.:0,0,0,.,.,.
2 15884079 . T C . PASS AF=0.667;AN=10;BaseQRankSum=0.203;ClippingRankSum=0.00 GT:PI:GQ:PL ./.:.:.:0,0,0 ./.:.:.:0,0,0
2 15884083 . T C . PASS AF=0.400;AN=14;BaseQRankSum=.;ClippingRankSum=. GT:PI:GQ:PL 1/1:4:21:271,21,0 0/0:7:3:.,.,.
2 15884088 . TA T . PASS AF=0.357;AN=12;BaseQRankSum=-8.290e-01;ClippingRankSum=0.00 GT:PI:GQ:PL ./.:.:.:0,0,0 0/0:7:6:.,.,.
2 15884090 . ATG A . PASS AF=0.545;AN=12;BaseQRankSum=.;ClippingRankSum=. GT:PI:GQ:PL 1/1:4:18:256,18,0 0/0:7:6:.,.,.
2 15884096 . G A . PASS AF=0.500;AN=14;BaseQRankSum=-7.010e-01;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:15:0,15,225 0/0:7:6:0,6,68
2 15884302 . G T . PASS AF=0.167;AN=12;BaseQRankSum=1.96;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:21:0,21,256 0/1:5:99:117,0,314
2 15884304 . G T . PASS AF=0.167;AN=12;BaseQRankSum=1.96;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:21:0,21,256 0/1:5:99:117,0,314
2 15884323 . G A . PASS AF=0.167;AN=12;BaseQRankSum=0.524;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:21:0,21,248 0/1:5:99:120,0,230
2 15884440 . GTT G . PASS AF=0.063;AN=14;BaseQRankSum=-3.450e-01;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:1:0,1,132 0/0:5:9:.,.,.
2 15884456 . TTTTTCACTGCG T,CTTTTCACTGCG . PASS AF=0.045,0.045;AN=12;BaseQRankSum=.;ClippingRankSum=. GT:PI:GQ:PL 0/0:4:18:0,18,270,18,270,270 0/0:5:18:.,.,.,.,.,.
2 15884457 . TTTTCACTGCG T,* . PASS AF=0.250,0.031;AN=14;BaseQRankSum=1.52;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:18:0,18,270,18,270,270 0/0:5:18:.,.,.,.,.,.
2 15884525 . G GAT . PASS AF=0.167;AN=12;BaseQRankSum=-8.420e-01;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:24:0,24,360 0/1:.:70:113,0,70
2 15884546 . G A . PASS AF=0.167;AN=12;BaseQRankSum=1.53;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:21:0,21,315 0/0:5:9:0,9,94
2 15884550 . G GT . PASS AF=0.033;AN=12;BaseQRankSum=-1.577e+00;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:18:0,18,270 0/0:5:12:.,.,.
2 15884582 . T C . PASS AF=1.00;AN=14;BaseQRankSum=.;ClippingRankSum=. GT:PI:GQ:PL 1/1:4:12:174,12,0 1/1:5:15:144,15,0
2 15884613 . G GTT . PASS AF=0.031;AN=14;BaseQRankSum=0.140;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:21:0,21,232 0/0:5:0:.,.,.
2 15884649 . G C . PASS AF=0.125;AN=14;BaseQRankSum=-1.981e+00;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:21:.,.,. 0/0:5:33:0,33,409
2 15884742 . A G . PASS AF=0.125;AN=14;BaseQRankSum=0.441;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:21:0,21,241 0/0:5:99:0,120,1800
2 15884746 . C A . PASS AF=0.125;AN=14;BaseQRankSum=0.817;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:21:0,21,241 0/0:5:99:0,120,1800
2 15884749 . T G . PASS AF=1.00;AN=14;BaseQRankSum=.;ClippingRankSum=. GT:PI:GQ:PL 1/1:4:24:360,24,0 1/1:5:99:16234,1262,0
2 15884753 . G C,GTCC . PASS AF=0.750,0.125;AN=14;BaseQRankSum=2.20;ClippingRankSum=0.00 GT:PI:GQ:PL 1/1:4:24:360,24,0,360,24,360 0/1:.:99:4817,0,6022,5642,6134,12537
2 15884873 . G GGAA . PASS AF=0.125;AN=14;BaseQRankSum=1.07;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:21:0,21,264 0/1:.:99:2473,0,3730
2 15884958 . T G . PASS AF=0.125;AN=14;BaseQRankSum=-2.330e+00;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:24:.,.,. 0/0:5:99:0,99,1485
2 15884965 . A G . PASS AF=0.042;AN=14;BaseQRankSum=0.00;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:33:0,33,443 0/0:5:99:.,.,.
2 15885010 . TCAA T . PASS AF=0.125;AN=14;BaseQRankSum=1.08;ClippingRankSum=0.00 GT:PI:GQ:PL 0/0:4:30:0,30,337 0/0:5:21:0,21,315
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