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path_vcf.vcf
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path_vcf.vcf
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##fileformat=VCFv4.2
##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
##FILTER=<ID=LowQual,Description="Low quality">
##FILTER=<ID=VQSRTrancheINDEL99.00to99.90,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -7.6918 <= x < -1.0989">
##FILTER=<ID=VQSRTrancheINDEL99.90to100.00+,Description="Truth sensitivity tranche level for INDEL model at VQS Lod < -308.0078">
##FILTER=<ID=VQSRTrancheINDEL99.90to100.00,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -308.0078 <= x < -7.6918">
##FILTER=<ID=VQSRTrancheSNP99.90to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -3965.5054">
##FILTER=<ID=VQSRTrancheSNP99.90to100.00,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -3965.5054 <= x < -18.7958">
##FILTER=<ID=lowGQ,Description="GQ < 20.0">
##FORMAT=<ID=AD,Number=.,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=FT,Number=1,Type=String,Description="Genotype-level filter">
##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=PP,Number=G,Type=Integer,Description="Phred-scaled Posterior Genotype Probabilities">
##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.ApplyRecalibration.2=<ID=ApplyRecalibration,Version=3.5-0-ge91472d,Date="Fri Sep 28 20:59:59 MSK 2018",Epoch=1538157599346,CommandLineOptions="analysis_type=ApplyRecalibration input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/home/yabarbitov/reference/GATK_b37/human_g1k_v37.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 logging_level=INFO log_to_file=null help=false version=false input=[(RodBinding name=input source=wes_67.snp.recal.vcf)] recal_file=(RodBinding name=recal_file source=wes_67.indel.recal) tranches_file=wes_67.indel.tranches out=/net/110-7198-609.cc.spbu.ru/home/yabarbitov/exomes/wes_67/vcfs/wes_67.recal.vcf ts_filter_level=99.0 lodCutoff=null ignore_filter=null ignore_all_filters=false excludeFiltered=false mode=INDEL filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
##GATKCommandLine.ApplyRecalibration=<ID=ApplyRecalibration,Version=3.5-0-ge91472d,Date="Fri Sep 28 20:52:00 MSK 2018",Epoch=1538157120891,CommandLineOptions="analysis_type=ApplyRecalibration input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/home/yabarbitov/reference/GATK_b37/human_g1k_v37.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 logging_level=INFO log_to_file=null help=false version=false input=[(RodBinding name=input source=wes_67.raw.vcf)] recal_file=(RodBinding name=recal_file source=wes_67.snp.recal) tranches_file=wes_67.snp.tranches out=/net/110-7198-609.cc.spbu.ru/home/yabarbitov/exomes/wes_67/vcfs/wes_67.snp.recal.vcf ts_filter_level=99.9 lodCutoff=null ignore_filter=null ignore_all_filters=false excludeFiltered=false mode=SNP filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
##GATKCommandLine.CalculateGenotypePosteriors=<ID=CalculateGenotypePosteriors,Version=3.5-0-ge91472d,Date="Fri Sep 28 21:02:23 MSK 2018",Epoch=1538157743573,CommandLineOptions="analysis_type=CalculateGenotypePosteriors input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/home/yabarbitov/reference/GATK_b37/human_g1k_v37.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=wes_67.retained.vcf) supporting=[(RodBinding name=supporting source=/home/yabarbitov/reference/gatk-bundle-b37//1000G_phase3_v4_20130502.sites.vcf)] globalPrior=0.001 deNovoPrior=1.0E-6 numRefSamplesIfNoCall=0 defaultToAC=false ignoreInputSamples=false discoveredACpriorsOff=false skipPopulationPriors=false skipFamilyPriors=true out=/net/110-7198-609.cc.spbu.ru/home/yabarbitov/exomes/wes_67/vcfs/wes_67.GR.vcf filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
##GATKCommandLine.GenotypeGVCFs=<ID=GenotypeGVCFs,Version=3.5-0-ge91472d,Date="Fri Sep 28 17:37:36 MSK 2018",Epoch=1538145456745,CommandLineOptions="analysis_type=GenotypeGVCFs input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/home/yabarbitov/reference/GATK_b37/human_g1k_v37.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 logging_level=INFO log_to_file=null help=false version=false variant=[(RodBindingCollection [(RodBinding name=variant source=/home/yabarbitov/exomes/wes_11/vcfs/wes_11.sample_417.g.vcf), (RodBinding 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name=variant111 source=/home/yabarbitov/exomes/wes_67/vcfs/gvcfs/wes_67.sample_B1-0327.g.vcf), (RodBinding name=variant112 source=/home/yabarbitov/exomes/wes_67/vcfs/gvcfs/wes_67.sample_B4-0004.g.vcf), (RodBinding name=variant113 source=/home/yabarbitov/exomes/wes_67/vcfs/gvcfs/wes_67.sample_B4-0022.g.vcf), (RodBinding name=variant114 source=/home/yabarbitov/exomes/wes_67/vcfs/gvcfs/wes_67.sample_B4-0032.g.vcf), (RodBinding name=variant115 source=/home/yabarbitov/exomes/wes_67/vcfs/gvcfs/wes_67.sample_SMA2.g.vcf), (RodBinding name=variant116 source=/home/yabarbitov/exomes/wes_67/vcfs/gvcfs/wes_67.sample_SMA3.g.vcf)])] out=/net/110-7198-609.cc.spbu.ru/home/yabarbitov/exomes/wes_67/vcfs/wes_67.raw.vcf includeNonVariantSites=false uniquifySamples=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=2 annotation=[] group=[Standard] dbsnp=(RodBinding name= source=UNBOUND) filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.5-0-ge91472d,Date="Wed Feb 15 22:27:53 MSK 2017",Epoch=1487186873098,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[run_21.sample_CH00307.recal.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=[/Molly/barbitoff/reference/truseq.intervals] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/Molly/barbitoff/reference/GATK_b37/human_g1k_v37.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 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 logging_level=INFO log_to_file=null help=false version=false 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, StandardHCAnnotation] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true gcpHMM=10 pair_hmm_implementation=VECTOR_LOGLESS_CACHING pair_hmm_sub_implementation=ENABLE_ALL always_load_vector_logless_PairHMM_lib=false phredScaledGlobalReadMismappingRate=45 noFpga=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=false keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
##GATKCommandLine.SelectVariants=<ID=SelectVariants,Version=3.5-0-ge91472d,Date="Fri Sep 28 21:00:59 MSK 2018",Epoch=1538157659154,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/home/yabarbitov/reference/GATK_b37/human_g1k_v37.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=wes_67.recal.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/net/110-7198-609.cc.spbu.ru/home/yabarbitov/exomes/wes_67/vcfs/wes_67.retained.vcf sample_name=[] sample_expressions=[SB0-0005|SB1-0020|SB1-0327|SB4-0004|SB4-0022|SB4-0032|SSMA2|SSMA3] sample_file=null exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[vc.isNotFiltered()] invertselect=false excludeNonVariants=true 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 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">
##GATKCommandLine.VariantFiltration=<ID=VariantFiltration,Version=3.5-0-ge91472d,Date="Fri Sep 28 21:13:11 MSK 2018",Epoch=1538158391151,CommandLineOptions="analysis_type=VariantFiltration input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/home/yabarbitov/reference/GATK_b37/human_g1k_v37.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=wes_67.GR.vcf) mask=(RodBinding name= source=UNBOUND) out=/net/110-7198-609.cc.spbu.ru/home/yabarbitov/exomes/wes_67/vcfs/wes_67.GF.vcf filterExpression=[] filterName=[] genotypeFilterExpression=[GQ < 20.0] genotypeFilterName=[lowGQ] 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">
##GVCFBlock0-1=minGQ=0(inclusive),maxGQ=1(exclusive)
##GVCFBlock1-2=minGQ=1(inclusive),maxGQ=2(exclusive)
##GVCFBlock10-11=minGQ=10(inclusive),maxGQ=11(exclusive)
##GVCFBlock11-12=minGQ=11(inclusive),maxGQ=12(exclusive)
##GVCFBlock12-13=minGQ=12(inclusive),maxGQ=13(exclusive)
##GVCFBlock13-14=minGQ=13(inclusive),maxGQ=14(exclusive)
##GVCFBlock14-15=minGQ=14(inclusive),maxGQ=15(exclusive)
##GVCFBlock15-16=minGQ=15(inclusive),maxGQ=16(exclusive)
##GVCFBlock16-17=minGQ=16(inclusive),maxGQ=17(exclusive)
##GVCFBlock17-18=minGQ=17(inclusive),maxGQ=18(exclusive)
##GVCFBlock18-19=minGQ=18(inclusive),maxGQ=19(exclusive)
##GVCFBlock19-20=minGQ=19(inclusive),maxGQ=20(exclusive)
##GVCFBlock2-3=minGQ=2(inclusive),maxGQ=3(exclusive)
##GVCFBlock20-21=minGQ=20(inclusive),maxGQ=21(exclusive)
##GVCFBlock21-22=minGQ=21(inclusive),maxGQ=22(exclusive)
##GVCFBlock22-23=minGQ=22(inclusive),maxGQ=23(exclusive)
##GVCFBlock23-24=minGQ=23(inclusive),maxGQ=24(exclusive)
##GVCFBlock24-25=minGQ=24(inclusive),maxGQ=25(exclusive)
##GVCFBlock25-26=minGQ=25(inclusive),maxGQ=26(exclusive)
##GVCFBlock26-27=minGQ=26(inclusive),maxGQ=27(exclusive)
##GVCFBlock27-28=minGQ=27(inclusive),maxGQ=28(exclusive)
##GVCFBlock28-29=minGQ=28(inclusive),maxGQ=29(exclusive)
##GVCFBlock29-30=minGQ=29(inclusive),maxGQ=30(exclusive)
##GVCFBlock3-4=minGQ=3(inclusive),maxGQ=4(exclusive)
##GVCFBlock30-31=minGQ=30(inclusive),maxGQ=31(exclusive)
##GVCFBlock31-32=minGQ=31(inclusive),maxGQ=32(exclusive)
##GVCFBlock32-33=minGQ=32(inclusive),maxGQ=33(exclusive)
##GVCFBlock33-34=minGQ=33(inclusive),maxGQ=34(exclusive)
##GVCFBlock34-35=minGQ=34(inclusive),maxGQ=35(exclusive)
##GVCFBlock35-36=minGQ=35(inclusive),maxGQ=36(exclusive)
##GVCFBlock36-37=minGQ=36(inclusive),maxGQ=37(exclusive)
##GVCFBlock37-38=minGQ=37(inclusive),maxGQ=38(exclusive)
##GVCFBlock38-39=minGQ=38(inclusive),maxGQ=39(exclusive)
##GVCFBlock39-40=minGQ=39(inclusive),maxGQ=40(exclusive)
##GVCFBlock4-5=minGQ=4(inclusive),maxGQ=5(exclusive)
##GVCFBlock40-41=minGQ=40(inclusive),maxGQ=41(exclusive)
##GVCFBlock41-42=minGQ=41(inclusive),maxGQ=42(exclusive)
##GVCFBlock42-43=minGQ=42(inclusive),maxGQ=43(exclusive)
##GVCFBlock43-44=minGQ=43(inclusive),maxGQ=44(exclusive)
##GVCFBlock44-45=minGQ=44(inclusive),maxGQ=45(exclusive)
##GVCFBlock45-46=minGQ=45(inclusive),maxGQ=46(exclusive)
##GVCFBlock46-47=minGQ=46(inclusive),maxGQ=47(exclusive)
##GVCFBlock47-48=minGQ=47(inclusive),maxGQ=48(exclusive)
##GVCFBlock48-49=minGQ=48(inclusive),maxGQ=49(exclusive)
##GVCFBlock49-50=minGQ=49(inclusive),maxGQ=50(exclusive)
##GVCFBlock5-6=minGQ=5(inclusive),maxGQ=6(exclusive)
##GVCFBlock50-51=minGQ=50(inclusive),maxGQ=51(exclusive)
##GVCFBlock51-52=minGQ=51(inclusive),maxGQ=52(exclusive)
##GVCFBlock52-53=minGQ=52(inclusive),maxGQ=53(exclusive)
##GVCFBlock53-54=minGQ=53(inclusive),maxGQ=54(exclusive)
##GVCFBlock54-55=minGQ=54(inclusive),maxGQ=55(exclusive)
##GVCFBlock55-56=minGQ=55(inclusive),maxGQ=56(exclusive)
##GVCFBlock56-57=minGQ=56(inclusive),maxGQ=57(exclusive)
##GVCFBlock57-58=minGQ=57(inclusive),maxGQ=58(exclusive)
##GVCFBlock58-59=minGQ=58(inclusive),maxGQ=59(exclusive)
##GVCFBlock59-60=minGQ=59(inclusive),maxGQ=60(exclusive)
##GVCFBlock6-7=minGQ=6(inclusive),maxGQ=7(exclusive)
##GVCFBlock60-70=minGQ=60(inclusive),maxGQ=70(exclusive)
##GVCFBlock7-8=minGQ=7(inclusive),maxGQ=8(exclusive)
##GVCFBlock70-80=minGQ=70(inclusive),maxGQ=80(exclusive)
##GVCFBlock8-9=minGQ=8(inclusive),maxGQ=9(exclusive)
##GVCFBlock80-90=minGQ=80(inclusive),maxGQ=90(exclusive)
##GVCFBlock9-10=minGQ=9(inclusive),maxGQ=10(exclusive)
##GVCFBlock90-99=minGQ=90(inclusive),maxGQ=99(exclusive)
##GVCFBlock99-2147483647=minGQ=99(inclusive),maxGQ=2147483647(exclusive)
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
##INFO=<ID=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">
##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=NEGATIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the negative training set of bad variants">
##INFO=<ID=PG,Number=G,Type=Integer,Description="Genotype Likelihood Prior">
##INFO=<ID=POSITIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the positive training set of good variants">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=RAW_MQ,Number=1,Type=Float,Description="Raw data for RMS Mapping Quality">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
##INFO=<ID=VQSLOD,Number=1,Type=Float,Description="Log odds of being a true variant versus being false under the trained gaussian mixture model">
##INFO=<ID=culprit,Number=1,Type=String,Description="The annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out">
##contig=<ID=1,length=249250621,assembly=b37>
##contig=<ID=2,length=243199373,assembly=b37>
##contig=<ID=3,length=198022430,assembly=b37>
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##contig=<ID=5,length=180915260,assembly=b37>
##contig=<ID=6,length=171115067,assembly=b37>
##contig=<ID=7,length=159138663,assembly=b37>
##contig=<ID=8,length=146364022,assembly=b37>
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##contig=<ID=11,length=135006516,assembly=b37>
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##contig=<ID=13,length=115169878,assembly=b37>
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##contig=<ID=17,length=81195210,assembly=b37>
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##contig=<ID=22,length=51304566,assembly=b37>
##contig=<ID=X,length=155270560,assembly=b37>
##contig=<ID=Y,length=59373566,assembly=b37>
##contig=<ID=MT,length=16569,assembly=b37>
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##contig=<ID=GL000246.1,length=38154,assembly=b37>
##contig=<ID=GL000249.1,length=38502,assembly=b37>
##contig=<ID=GL000196.1,length=38914,assembly=b37>
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##contig=<ID=GL000206.1,length=41001,assembly=b37>
##contig=<ID=GL000240.1,length=41933,assembly=b37>
##contig=<ID=GL000236.1,length=41934,assembly=b37>
##contig=<ID=GL000241.1,length=42152,assembly=b37>
##contig=<ID=GL000243.1,length=43341,assembly=b37>
##contig=<ID=GL000242.1,length=43523,assembly=b37>
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##contig=<ID=GL000218.1,length=161147,assembly=b37>
##contig=<ID=GL000220.1,length=161802,assembly=b37>
##contig=<ID=GL000213.1,length=164239,assembly=b37>
##contig=<ID=GL000211.1,length=166566,assembly=b37>
##contig=<ID=GL000199.1,length=169874,assembly=b37>
##contig=<ID=GL000217.1,length=172149,assembly=b37>
##contig=<ID=GL000216.1,length=172294,assembly=b37>
##contig=<ID=GL000215.1,length=172545,assembly=b37>
##contig=<ID=GL000205.1,length=174588,assembly=b37>
##contig=<ID=GL000219.1,length=179198,assembly=b37>
##contig=<ID=GL000224.1,length=179693,assembly=b37>
##contig=<ID=GL000223.1,length=180455,assembly=b37>
##contig=<ID=GL000195.1,length=182896,assembly=b37>
##contig=<ID=GL000212.1,length=186858,assembly=b37>
##contig=<ID=GL000222.1,length=186861,assembly=b37>
##contig=<ID=GL000200.1,length=187035,assembly=b37>
##contig=<ID=GL000193.1,length=189789,assembly=b37>
##contig=<ID=GL000194.1,length=191469,assembly=b37>
##contig=<ID=GL000225.1,length=211173,assembly=b37>
##contig=<ID=GL000192.1,length=547496,assembly=b37>
##reference=file:///home/yabarbitov/reference/GATK_b37/human_g1k_v37.fasta
##source=CalculateGenotypePosteriors
##source=SelectVariants
##SnpSiftVersion="SnpSift 4.2 (build 2015-12-05), by Pablo Cingolani"
##SnpSiftCmd="SnpSift annotate -noInfo /home/yabarbitov/reference/dbSNP_b150.vcf wes_67.S1.vcf"
##SnpSiftCmd="SnpSift annotate -noId -info PM,OM,CLNSIG,CLNDBN,CLNREVSTAT /home/yabarbitov/reference/clinvar_20170530.vcf wes_67.S2.vcf"
##INFO=<ID=CLNSIG,Number=.,Type=String,Description="Variant Clinical Significance, 0 - Uncertain significance, 1 - not provided, 2 - Benign, 3 - Likely benign, 4 - Likely pathogenic, 5 - Pathogenic, 6 - drug response, 7 - histocompatibility, 255 - other">
##INFO=<ID=CLNREVSTAT,Number=.,Type=String,Description="no_assertion - No assertion provided, no_criteria - No assertion criteria provided, single - Criteria provided single submitter, mult - Criteria provided multiple submitters no conflicts, conf - Criteria provided conflicting interpretations, exp - Reviewed by expert panel, guideline - Practice guideline">
##INFO=<ID=CLNDBN,Number=.,Type=String,Description="Variant disease name">
##INFO=<ID=OM,Number=0,Type=Flag,Description="Has OMIM/OMIA">
##INFO=<ID=PM,Number=0,Type=Flag,Description="Variant is Precious(Clinical,Pubmed Cited)">
##SnpSiftCmd="SnpSift annotate -noId -info X1000Gp3_AF /home/yabarbitov/reference/1000G_phase3_v4_20130502.sites.vcf wes_67.S3.vcf"
##INFO=<ID=X1000Gp3_AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">
##SnpSiftCmd="SnpSift annotate -noId -info ExAC_AF /home/yabarbitov/reference/ExAC.r0.3.1.sites.vep.vcf wes_67.S4.vcf"
##INFO=<ID=ExAC_AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##SnpSiftCmd="SnpSift annotate -noId -info ESP6500_AF /home/yabarbitov/reference/ESP6500.sites.vcf wes_67.S5.vcf"
##INFO=<ID=ESP6500_AF,Number=.,Type=String,Description="Minor Allele Frequency in percent in the order of EA,AA,All">
##SnpSiftCmd="SnpSift annotate -noId -info BIOBANK_AF_v20171101 /home/yabarbitov/reference/BIOBANK_v20171101_sites.vcf wes_67.S6.vcf"
##INFO=<ID=BIOBANK_AF_v20171101,Number=A,Type=Float,Description="Allele Frequency in the SPBU BIOBANK (collected 2017-11-01 (570 samples)">
##SnpSiftCmd="SnpSift gwasCat wes_67.S7.vcf"
##INFO=<ID=GWASCAT_TRAIT,Number=.,Type=String,Description="GWAS catalog: Associated trait">
##INFO=<ID=GWASCAT_P_VALUE,Number=.,Type=Float,Description="GWAS catalog: p-value">
##INFO=<ID=GWASCAT_OR_BETA,Number=.,Type=Float,Description="GWAS catalog: OR or Beta">
##INFO=<ID=GWASCAT_REPORTED_GENE,Number=.,Type=String,Description="GWAS catalog: Reported gene">
##INFO=<ID=GWASCAT_PUBMED_ID,Number=.,Type=String,Description="GWAS catalog: Original paper's Pubmed ID">
##SnpSiftCmd="SnpSift dbnsfp -f PROVEAN_pred,SIFT_pred,Polyphen2_HVAR_pred wes_67.S9.vcf"
##INFO=<ID=dbNSFP_Polyphen2_HVAR_pred,Number=A,Type=Character,Description="Field 'Polyphen2_HVAR_pred' from dbNSFP">
##INFO=<ID=dbNSFP_PROVEAN_pred,Number=A,Type=Character,Description="Field 'PROVEAN_pred' from dbNSFP">
##INFO=<ID=dbNSFP_SIFT_pred,Number=A,Type=Character,Description="Field 'SIFT_pred' from dbNSFP">
##SnpEffVersion="4.2 (build 2015-12-05), by Pablo Cingolani"
##SnpEffCmd="SnpEff hg19 wes_67.S10.vcf "
##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' ">
##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected' ">
##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected' ">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SB0-0005 SB1-0020 SB1-0327 SB4-0004 SB4-0022 SB4-0032 SSMA2 SSMA3
1 115222237 rs34526199 T A 42754.72 PASS AF=0.063;FS=0.000;MQ=60.00;QD=11.61;VQSLOD=12.25;CLNDBN=Muscle_AMP_deaminase_deficiency;CLNREVSTAT=single;CLNSIG=5;PM;X1000Gp3_AF=0.0109824;ExAC_AF=0.028;ESP6500_AF=0.0241427;BIOBANK_AF_v20171101=0.056;dbNSFP_PROVEAN_pred=D,D,D;dbNSFP_Polyphen2_HVAR_pred=D,D;dbNSFP_SIFT_pred=D,D,D;ANN=A|missense_variant|MODERATE|AMPD1|AMPD1|transcript|NM_000036|protein_coding|7/16|c.959A>T|p.Lys320Ile|1007/2406|959/2343|320/780||,A|missense_variant|MODERATE|AMPD1|AMPD1|transcript|NM_001172626|protein_coding|6/15|c.947A>T|p.Lys316Ile|995/2394|947/2331|316/776|| GT:AD:DP:GQ:PL:PP 0/0:39,0:39:99:0,105,1575:0,121,1614 0/0:38,0:38:99:0,103,1058:0,119,1097 0/0:36,0:36:99:0,107,931:0,123,970 0/0:37,0:37:99:0,111,966:0,127,1005 0/1:30,35:65:99:754,0,613:738,0,635 0/0:35,0:35:99:0,102,968:0,118,1007 0/0:40,0:40:99:0,120,1100:0,136,1139 0/0:41,0:41:99:0,120,1800:0,136,1839
1 145507765 rs201779890 G C 2001.97 PASS AF=0.125;FS=1.815;MQ=59.97;QD=10.71;VQSLOD=1.78;CLNDBN=Radial_aplasia-thrombocytopenia_syndrome|not_provided;CLNREVSTAT=single|conf;CLNSIG=5|255;OM;PM;X1000Gp3_AF=0.000798722;ExAC_AF=5.349e-03;ESP6500_AF=0.00492081;BIOBANK_AF_v20171101=0.017;ANN=C|downstream_gene_variant|MODIFIER|GNRHR2|GNRHR2|transcript|NR_002328|pseudogene||n.*1987C>G|||||1987|,C|downstream_gene_variant|MODIFIER|GNRHR2|GNRHR2|transcript|NR_104033|pseudogene||n.*1987C>G|||||1987|,C|intron_variant|MODIFIER|NBPF20|NBPF20|transcript|NM_001278267|protein_coding|99/130|c.10988+143091G>C||||||,C|intron_variant|MODIFIER|NBPF10|NBPF10|transcript|NM_001302371|protein_coding|68/89|c.8614+142306G>C||||||,C|intron_variant|MODIFIER|RBM8A|RBM8A|transcript|NM_005105|protein_coding|1/5|c.67+32G>C||||||,C|intron_variant|MODIFIER|NBPF10|NBPF10|transcript|NM_001039703|protein_coding|68/85|c.8614+142306G>C|||||| GT:AD:DP:GQ:PL:PP 0/0:43,0:43:99:0,102,1530:0,128,1588 0/1:18,27:45:99:539,0,304:513,0,336 0/1:38,38:76:99:785,0,732:759,0,764 0/0:34,0:34:99:0,102,865:0,128,923 0/0:35,0:35:99:0,99,947:0,125,1005 0/0:36,0:36:99:0,105,1002:0,131,1060 0/0:39,0:39:99:0,111,1038:0,137,1096 0/0:37,0:37:99:0,110,916:0,136,974
1 159175494 rs34599082 C T 3912.16 PASS AF=0.063;FS=0.409;MQ=60.00;QD=12.30;VQSLOD=10.04;CLNDBN=DUFFY_BLOOD_GROUP_SYSTEM\x2c_FY(bwk)_PHENOTYPE;CLNREVSTAT=no_criteria;CLNSIG=5;OM;PM;X1000Gp3_AF=0.00459265;ExAC_AF=0.011;ESP6500_AF=0.0109949;BIOBANK_AF_v20171101=0.029;dbNSFP_PROVEAN_pred=N,N,N,N,N;dbNSFP_Polyphen2_HVAR_pred=P,P;dbNSFP_SIFT_pred=T,T,T,T,T;ANN=T|missense_variant|MODERATE|ACKR1|ACKR1|transcript|NM_001122951|protein_coding|1/1|c.271C>T|p.Arg91Cys|446/1242|271/1017|91/338||,T|missense_variant|MODERATE|ACKR1|ACKR1|transcript|NM_002036|protein_coding|2/2|c.265C>T|p.Arg89Cys|1212/2008|265/1011|89/336||,T|upstream_gene_variant|MODIFIER|CADM3-AS1|CADM3-AS1|transcript|NR_037870|pseudogene||n.-3282G>A|||||3282|,T|downstream_gene_variant|MODIFIER|CADM3|CADM3|transcript|NM_021189|protein_coding||c.*4782C>T|||||2562|,T|downstream_gene_variant|MODIFIER|CADM3|CADM3|transcript|NM_001127173|protein_coding||c.*4782C>T|||||2562| GT:AD:DP:GQ:PL:PP 0/0:52,0:52:99:0,120,1800:0,140,1846 0/0:84,0:84:99:0,120,1800:0,140,1846 0/0:59,0:59:99:0,120,1800:0,140,1846 0/0:44,0:44:99:0,111,1665:0,131,1711 0/0:128,0:128:99:0,120,1800:0,140,1846 0/1:39,46:85:99:1194,0,878:1174,0,904 0/0:43,0:43:99:0,105,1575:0,125,1621 0/0:44,0:44:99:0,99,1485:0,119,1531
1 227170648 rs41303129 C T 6661.16 PASS AF=0.063;FS=1.104;MQ=60.00;QD=10.20;VQSLOD=11.44;CLNDBN=Coenzyme_Q10_deficiency\x2c_primary\x2c_4|not_specified|Spinocerebellar_Ataxia\x2c_Recessive|not_provided;CLNREVSTAT=no_criteria|mult|single|single;CLNSIG=5|2|3|0;OM;PM;X1000Gp3_AF=0.00559105;ExAC_AF=0.016;ESP6500_AF=0.0150046;BIOBANK_AF_v20171101=0.011;ANN=T|synonymous_variant|LOW|ADCK3|ADCK3|transcript|NM_020247|protein_coding|8/15|c.993C>T|p.Phe331Phe|1165/2924|993/1944|331/647|| GT:AD:DP:GQ:PL:PP 0/0:148,0:148:99:0,120,1800:0,139,1845 0/0:178,0:178:99:0,120,1800:0,139,1845 0/0:231,0:231:99:0,120,1800:0,139,1845 0/0:144,0:144:99:0,120,1800:0,139,1845 0/0:224,0:224:99:0,120,1800:0,139,1845 0/0:195,0:195:99:0,120,1800:0,139,1845 0/1:260,216:476:99:4447,0,5569:4428,0,5594 0/0:188,0:188:99:0,120,1800:0,139,1845
2 25457242 rs147001633 C T 168.18 PASS AF=0.063;FS=0.000;MQ=60.00;QD=2.16;VQSLOD=10.71;CLNDBN=Acute_myeloid_leukemia,Adenocarcinoma_of_lung|Myelodysplastic_syndrome|Acute_myeloid_leukemia,Adenocarcinoma_of_lung|Acute_myeloid_leukemia|Myelodysplastic_syndrome|not_provided;CLNREVSTAT=no_criteria,no_criteria|no_criteria|no_criteria,no_criteria|no_criteria|no_criteria|single;CLNSIG=5,4|4|5,4|5|4|5;ExAC_AF=5.930e-04;ESP6500_AF=0.000691988;dbNSFP_PROVEAN_pred=D,D,D,D;dbNSFP_Polyphen2_HVAR_pred=B,B;dbNSFP_SIFT_pred=D,D,D,D;ANN=T|missense_variant|MODERATE|DNMT3A|DNMT3A|transcript|NM_022552|protein_coding|23/23|c.2645G>A|p.Arg882His|2912/4324|2645/2739|882/912||,T|missense_variant|MODERATE|DNMT3A|DNMT3A|transcript|NM_001320893|protein_coding|18/18|c.2189G>A|p.Arg730His|2226/3638|2189/2283|730/760||,T|missense_variant|MODERATE|DNMT3A|DNMT3A|transcript|NM_153759|protein_coding|19/19|c.2078G>A|p.Arg693His|2196/3608|2078/2172|693/723||,T|missense_variant|MODERATE|DNMT3A|DNMT3A|transcript|NM_175629|protein_coding|23/23|c.2645G>A|p.Arg882His|2983/4395|2645/2739|882/912||,T|non_coding_exon_variant|MODIFIER|DNMT3A|DNMT3A|transcript|NR_135490|pseudogene|24/24|n.3182G>A|||||| GT:AD:DP:GQ:PL:PP 0/0:34,0:34:99:0,99,1485:0,99,1485 0/0:41,0:41:99:0,105,1575:0,105,1575 0/0:39,0:39:99:0,99,1162:0,99,1162 0/0:36,0:36:99:0,99,950:0,99,950 0/1:60,18:78:99:211,0,1381:211,0,1381 0/0:34,0:34:99:0,102,916:0,102,916 0/0:45,0:45:99:0,109,1326:0,109,1326 0/0:42,0:42:99:0,105,1350:0,105,1350
2 48025764 rs1800937 C T 28508.55 PASS AF=0.250;FS=1.794;MQ=59.99;QD=13.60;VQSLOD=5.05;CLNDBN=Lynch_syndrome,Lynch_syndrome|not_provided,Lynch_syndrome|not_specified|Hereditary_cancer-predisposing_syndrome;CLNREVSTAT=exp,exp|single,exp|mult|mult;CLNSIG=5,5|5,2|2|2;PM;X1000Gp3_AF=0.0285543;ExAC_AF=0.072;ESP6500_AF=0.0691219;BIOBANK_AF_v20171101=0.109;ANN=T|synonymous_variant|LOW|MSH6|MSH6|transcript|NM_000179|protein_coding|4/10|c.642C>T|p.Tyr214Tyr|794/4328|642/4083|214/1360||,T|synonymous_variant|LOW|MSH6|MSH6|transcript|NM_001281492|protein_coding|2/8|c.252C>T|p.Tyr84Tyr|404/3938|252/3693|84/1230||,T|5_prime_UTR_premature_start_codon_gain_variant|LOW|MSH6|MSH6|transcript|NM_001281493|protein_coding|3/9|c.-265C>T||||||,T|5_prime_UTR_premature_start_codon_gain_variant|LOW|MSH6|MSH6|transcript|NM_001281494|protein_coding|4/10|c.-265C>T||||||,T|5_prime_UTR_variant|MODIFIER|MSH6|MSH6|transcript|NM_001281493|protein_coding|3/9|c.-265C>T|||||265|,T|5_prime_UTR_variant|MODIFIER|MSH6|MSH6|transcript|NM_001281494|protein_coding|4/10|c.-265C>T|||||265| GT:AD:DP:GQ:PL:PP 0/0:27,0:27:93:0,81,699:0,93,729 0/1:10,21:31:99:509,0,154:497,0,172 1/1:0,34:34:84:997,102,0:967,84,0 0/1:12,8:20:99:164,0,262:152,0,280 0/0:34,0:34:99:0,99,1485:0,111,1515 0/0:31,0:31:99:0,90,824:0,102,854 0/0:24,0:24:84:0,72,627:0,84,657 0/0:24,0:24:52:0,40,630:0,52,660
2 71337204 rs138436961 G A 7562.82 PASS AF=0.125;FS=1.745;MQ=60.00;QD=9.78;VQSLOD=6.44;CLNDBN=Methylmalonyl-CoA_epimerase_deficiency;CLNREVSTAT=no_criteria;CLNSIG=5;X1000Gp3_AF=0.000998403;ExAC_AF=5.247e-03;ESP6500_AF=0.00538213;BIOBANK_AF_v20171101=5.703e-03;dbNSFP_PROVEAN_pred=D,D;dbNSFP_Polyphen2_HVAR_pred=D;dbNSFP_SIFT_pred=D,D;ANN=A|missense_variant|MODERATE|MCEE|MCEE|transcript|NM_032601|protein_coding|3/3|c.427C>T|p.Arg143Cys|472/870|427/531|143/176|| GT:AD:DP:GQ:PL:PP 0/1:45,30:75:99:555,0,896:529,0,927 0/0:45,0:45:99:0,116,1249:0,142,1306 0/0:38,0:38:99:0,102,1040:0,128,1097 0/1:33,28:61:99:568,0,667:542,0,698 0/0:37,0:37:99:0,99,1485:0,125,1542 0/0:35,0:35:99:0,102,1530:0,128,1587 0/0:34,0:34:99:0,102,865:0,128,922 0/0:44,0:44:99:0,108,1239:0,134,1296
2 233390199 rs61744404 C G 9600.42 PASS AF=0.188;FS=0.000;MQ=59.91;QD=14.22;VQSLOD=1.76;CLNDBN=Microphthalmia\x2c_isolated_6|not_specified;CLNREVSTAT=no_criteria|single;CLNSIG=5|2;OM;PM;X1000Gp3_AF=0.0213658;ExAC_AF=0.037;BIOBANK_AF_v20171101=0.048;ANN=G|missense_variant|MODERATE|PRSS56|PRSS56|transcript|NM_001195129|protein_coding|13/13|c.1795C>G|p.Pro599Ala|1931/2157|1795/1812|599/603||,G|upstream_gene_variant|MODIFIER|CHRND|CHRND|transcript|NM_000751|protein_coding||c.-727C>G|||||671|,G|upstream_gene_variant|MODIFIER|CHRND|CHRND|transcript|NM_001256657|protein_coding||c.-727C>G|||||671|,G|upstream_gene_variant|MODIFIER|CHRND|CHRND|transcript|NM_001311195|protein_coding||c.-2801C>G|||||671|,G|upstream_gene_variant|MODIFIER|CHRND|CHRND|transcript|NM_001311196|protein_coding||c.-2801C>G|||||671| GT:AD:DP:GQ:PL:PP 0/1:80,48:128:99:811,0,1674:798,0,1693 0/0:116,0:116:99:0,120,1800:0,133,1833 1/1:0,145:145:99:3798,433,0:3765,414,0 0/0:71,0:71:99:0,120,1800:0,133,1833 0/0:108,0:108:99:0,120,1800:0,133,1833 0/0:89,0:89:99:0,120,1800:0,133,1833 0/0:88,0:88:99:0,120,1800:0,133,1833 0/0:72,0:72:99:0,120,1800:0,133,1833
2 238242176 rs182976977 G C 577.18 PASS AF=0.063;FS=2.021;MQ=60.00;QD=8.75;VQSLOD=5.19;CLNDBN=Dystonia_27|not_specified|Collagen_VI-related_myopathy;CLNREVSTAT=no_criteria|mult|single;CLNSIG=5|3|3;PM;X1000Gp3_AF=0.000399361;ExAC_AF=9.719e-04;ESP6500_AF=0.000615101;dbNSFP_PROVEAN_pred=N,N,N,N,N,N;dbNSFP_Polyphen2_HVAR_pred=B,B,B;dbNSFP_SIFT_pred=D,D,D,T,D,D;ANN=C|missense_variant|MODERATE|COL6A3|COL6A3|transcript|NM_004369|protein_coding|42/44|c.9245C>G|p.Pro3082Arg|9530/10581|9245/9534|3082/3177||,C|missense_variant|MODERATE|COL6A3|COL6A3|transcript|NM_057166|protein_coding|39/41|c.7424C>G|p.Pro2475Arg|7709/8760|7424/7713|2475/2570||,C|missense_variant|MODERATE|COL6A3|COL6A3|transcript|NM_057167|protein_coding|41/43|c.8627C>G|p.Pro2876Arg|8912/9963|8627/8916|2876/2971|| GT:AD:DP:GQ:PL:PP 0/1:35,31:66:99:620,0,680:591,0,714 0/0:61,0:61:99:0,120,1800:0,149,1863 0/0:50,0:50:99:0,114,1710:0,143,1773 0/0:44,0:44:99:0,105,1575:0,134,1638 0/0:65,0:65:99:0,120,1800:0,149,1863 0/0:40,0:40:99:0,108,1620:0,137,1683 0/0:55,0:55:99:0,120,1800:0,149,1863 0/0:46,0:46:99:0,120,1800:0,149,1863
3 39307162 rs3732378 G A 21284.51 PASS AF=0.125;FS=0.000;MQ=60.00;QD=13.38;VQSLOD=14.22;CLNDBN=Human_immunodeficiency_virus_type_1\x2c_rapid_progression_to_AIDS|Coronary_artery_disease\x2c_resistance_to|Age-related_macular_degeneration_12|MACULAR_DEGENERATION\x2c_AGE-RELATED\x2c_12\x2c_SUSCEPTIBILITY_TO;CLNREVSTAT=no_criteria|no_criteria|no_criteria|no_criteria;CLNSIG=5|255|255|255;OM;PM;X1000Gp3_AF=0.0854633;ExAC_AF=0.136;ESP6500_AF=0.127371;BIOBANK_AF_v20171101=0.209;dbNSFP_PROVEAN_pred=D,D,D,D,D;dbNSFP_Polyphen2_HVAR_pred=B;dbNSFP_SIFT_pred=D,D,T,D,D;ANN=A|missense_variant|MODERATE|CX3CR1|CX3CR1|transcript|NM_001171174|protein_coding|2/2|c.935C>T|p.Thr312Met|975/3152|935/1164|312/387||,A|missense_variant|MODERATE|CX3CR1|CX3CR1|transcript|NM_001337|protein_coding|2/2|c.839C>T|p.Thr280Met|931/3108|839/1068|280/355||,A|missense_variant|MODERATE|CX3CR1|CX3CR1|transcript|NM_001171172|protein_coding|2/2|c.839C>T|p.Thr280Met|1039/3216|839/1068|280/355||,A|missense_variant|MODERATE|CX3CR1|CX3CR1|transcript|NM_001171171|protein_coding|2/2|c.839C>T|p.Thr280Met|1079/3256|839/1068|280/355|| GT:AD:DP:GQ:PL:PP 0/1:33,32:65:99:610,0,657:603,0,670 0/0:35,0:35:99:0,105,969:0,112,990 0/0:34,0:34:99:0,99,1006:0,106,1027 0/1:20,25:45:99:544,0,469:537,0,482 0/0:43,0:43:99:0,106,1202:0,113,1223 0/0:45,0:45:99:0,105,1439:0,112,1460 0/0:39,0:39:99:0,99,1281:0,106,1302 0/0:42,0:42:99:0,102,1280:0,109,1301
3 39307256 rs3732379 C T 54565.36 PASS AF=0.125;FS=0.000;MQ=60.00;QD=13.49;VQSLOD=14.00;CLNDBN=Human_immunodeficiency_virus_type_1\x2c_rapid_progression_to_AIDS|Coronary_artery_disease\x2c_resistance_to|Age-related_macular_degeneration_12|MACULAR_DEGENERATION\x2c_AGE-RELATED\x2c_12\x2c_SUSCEPTIBILITY_TO;CLNREVSTAT=no_criteria|no_criteria|no_criteria|no_criteria;CLNSIG=5|255|255|255;OM;PM;X1000Gp3_AF=0.144369;ExAC_AF=0.221;ESP6500_AF=0.231074;BIOBANK_AF_v20171101=0.277;dbNSFP_PROVEAN_pred=N,N,N,N,N;dbNSFP_Polyphen2_HVAR_pred=B;dbNSFP_SIFT_pred=T,T,T,T,T;ANN=T|missense_variant|MODERATE|CX3CR1|CX3CR1|transcript|NM_001171174|protein_coding|2/2|c.841G>A|p.Val281Ile|881/3152|841/1164|281/387||,T|missense_variant|MODERATE|CX3CR1|CX3CR1|transcript|NM_001337|protein_coding|2/2|c.745G>A|p.Val249Ile|837/3108|745/1068|249/355||,T|missense_variant|MODERATE|CX3CR1|CX3CR1|transcript|NM_001171172|protein_coding|2/2|c.745G>A|p.Val249Ile|945/3216|745/1068|249/355||,T|missense_variant|MODERATE|CX3CR1|CX3CR1|transcript|NM_001171171|protein_coding|2/2|c.745G>A|p.Val249Ile|985/3256|745/1068|249/355|| GT:AD:DP:GQ:PL:PP 0/1:26,28:54:99:567,0,516:562,0,527 0/0:35,0:35:99:0,105,969:0,110,984 0/0:34,0:34:99:0,99,1006:0,104,1021 0/1:33,42:75:99:885,0,659:880,0,670 0/0:43,0:43:99:0,106,1202:0,111,1217 0/0:45,0:45:99:0,105,1439:0,110,1454 0/0:39,0:39:99:0,99,1281:0,104,1296 0/0:42,0:42:99:0,102,1280:0,107,1295
3 132408107 rs751527253 CCT C 1465.13 PASS AF=0.063;FS=0.883;MQ=60.43;QD=19.80;VQSLOD=1.57;CLNDBN=Meckel_syndrome_type_7|Renal-hepatic-pancreatic_dysplasia|Nephronophthisis|Polycystic_kidney_dysplasia|not_provided;CLNREVSTAT=no_criteria|no_criteria|single|no_criteria|single;CLNSIG=5|5|5|5|5;PM;ExAC_AF=3.542e-04;ESP6500_AF=0.000239655;ANN=C|splice_acceptor_variant&intron_variant|HIGH|NPHP3-ACAD11|NPHP3-ACAD11|transcript|NR_037804|pseudogene|18/44|n.2700-2_2700-1delAG||||||,C|splice_acceptor_variant&intron_variant|HIGH|NPHP3|NPHP3|transcript|NM_153240|protein_coding|19/26|c.2694-2_2694-1delAG||||||;LOF=(NPHP3|NPHP3|1|1.00) GT:AD:DP:GQ:PL:PP 0/0:36,0:36:99:0,107,901:0,107,901 0/0:55,0:55:99:0,120,1800:0,120,1800 0/0:43,0:43:99:0,119,1386:0,119,1386 0/0:34,0:34:99:0,99,879:0,99,879 0/0:58,0:58:99:0,120,1800:0,120,1800 0/0:36,0:36:99:0,108,1030:0,108,1030 0/1:34,40:74:99:1517,0,1458:1517,0,1458 0/0:45,0:45:99:0,99,1080:0,99,1080
3 148895654 rs34394958 A G 31140.02 PASS AF=0.125;FS=0.523;MQ=60.00;QD=13.19;VQSLOD=11.70;CLNDBN=Deficiency_of_ferroxidase,not_specified|Deficiency_of_ferroxidase|Hermansky-Pudlak_syndrome;CLNREVSTAT=no_criteria,single|single|single;CLNSIG=5,2|3|3;PM;X1000Gp3_AF=0.019369;ExAC_AF=0.033;ESP6500_AF=0.031447;BIOBANK_AF_v20171101=0.036;ANN=G|synonymous_variant|LOW|CP|CP|transcript|NM_000096|protein_coding|17/19|c.2991T>C|p.His997His|3244/4662|2991/3198|997/1065||,G|downstream_gene_variant|MODIFIER|HPS3|HPS3|transcript|NM_032383|protein_coding||c.*5645A>G|||||4671|,G|downstream_gene_variant|MODIFIER|HPS3|HPS3|transcript|NM_001308258|protein_coding||c.*5645A>G|||||4671|,G|non_coding_exon_variant|MODIFIER|CP|CP|transcript|NR_046371|pseudogene|16/18|n.3031T>C|||||| GT:AD:DP:GQ:PL:PP 0/0:47,0:47:99:0,120,1800:0,134,1834 0/0:75,0:75:99:0,120,1800:0,134,1834 0/0:61,0:61:99:0,120,1800:0,134,1834 0/0:46,0:46:99:0,120,1800:0,134,1834 0/0:77,0:77:99:0,120,1800:0,134,1834 0/0:83,0:83:99:0,120,1800:0,134,1834 0/1:51,70:121:99:1490,0,1075:1476,0,1095 0/1:42,43:85:99:801,0,827:787,0,847
3 151055867 rs121917885 C T 498.18 PASS AF=0.063;FS=0.000;MQ=60.00;QD=6.31;VQSLOD=4.86;CLNDBN=Platelet-type_bleeding_disorder_8;CLNREVSTAT=no_criteria;CLNSIG=5;OM;PM;ExAC_AF=2.471e-05;dbNSFP_PROVEAN_pred=D,D;dbNSFP_Polyphen2_HVAR_pred=D;dbNSFP_SIFT_pred=D,D;ANN=T|missense_variant|MODERATE|P2RY12|P2RY12|transcript|NM_022788|protein_coding|3/3|c.767G>A|p.Arg256Gln|1067/2303|767/1029|256/342||,T|missense_variant|MODERATE|P2RY12|P2RY12|transcript|NM_176876|protein_coding|2/2|c.767G>A|p.Arg256Gln|1041/2277|767/1029|256/342||,T|intron_variant|MODIFIER|MED12L|MED12L|transcript|NM_053002|protein_coding|14/42|c.2146-11980C>T|||||| GT:AD:DP:GQ:PL:PP 0/1:49,30:79:99:541,0,975:541,0,975 0/0:56,0:56:99:0,120,1800:0,120,1800 0/0:57,0:57:99:0,120,1800:0,120,1800 0/0:41,0:41:99:0,117,1755:0,117,1755 0/0:68,0:68:99:0,120,1800:0,120,1800 0/0:55,0:55:99:0,120,1800:0,120,1800 0/0:34,0:34:99:0,102,937:0,102,937 0/0:38,0:38:99:0,114,977:0,114,977
3 165547569 rs28933390 C A 2325.73 PASS AF=0.063;FS=2.279;MQ=60.00;QD=10.34;VQSLOD=5.32;CLNDBN=BCHE\x2c_fluoride_2|Deficiency_of_butyrylcholine_esterase;CLNREVSTAT=no_criteria|conf;CLNSIG=5|255;OM;PM;X1000Gp3_AF=0.00199681;ExAC_AF=3.015e-03;ESP6500_AF=0.00361372;BIOBANK_AF_v20171101=6.641e-03;dbNSFP_PROVEAN_pred=N;dbNSFP_Polyphen2_HVAR_pred=B;dbNSFP_SIFT_pred=D;ANN=A|missense_variant|MODERATE|BCHE|BCHE|transcript|NM_000055|protein_coding|2/4|c.1253G>T|p.Gly418Val|1413/2447|1253/1809|418/602|| GT:AD:DP:GQ:PL:PP 0/1:29,20:49:99:344,0,576:320,0,605 0/0:37,0:37:99:0,99,998:0,123,1051 0/0:40,0:40:99:0,108,1620:0,132,1673 0/0:39,0:39:99:0,105,1575:0,129,1628 0/0:38,0:38:99:0,102,1530:0,126,1583 0/0:40,0:40:99:0,99,1485:0,123,1538 0/0:42,0:42:99:0,102,1530:0,126,1583 0/0:59,0:59:99:0,120,1800:0,144,1853
5 1272311 rs141425941 C T 891.18 PASS AF=0.063;FS=0.000;MQ=60.00;QD=11.43;VQSLOD=4.76;CLNDBN=Pulmonary_fibrosis_and/or_bone_marrow_failure\x2c_telomere-related\x2c_1|Dyskeratosis_congenita\x2c_autosomal_dominant\x2c_2|Idiopathic_fibrosing_alveolitis\x2c_chronic_form;CLNREVSTAT=no_criteria|single|single;CLNSIG=5|0|0;PM;ExAC_AF=1.407e-04;ESP6500_AF=0.000240308;dbNSFP_PROVEAN_pred=N,N;dbNSFP_Polyphen2_HVAR_pred=B,P;dbNSFP_SIFT_pred=T,T;ANN=T|missense_variant|MODERATE|TERT|TERT|transcript|NM_198253|protein_coding|7/16|c.2371G>A|p.Val791Ile|2429/4013|2371/3399|791/1132||,T|missense_variant|MODERATE|TERT|TERT|transcript|NM_001193376|protein_coding|7/15|c.2371G>A|p.Val791Ile|2429/3824|2371/3210|791/1069|| GT:AD:DP:GQ:PL:PP 0/0:43,0:43:99:0,120,1800:0,120,1800 0/0:62,0:62:99:0,120,1800:0,120,1800 0/0:45,0:45:99:0,120,1800:0,120,1800 0/0:46,0:46:99:0,120,1800:0,120,1800 0/0:50,0:50:99:0,102,1450:0,102,1450 0/0:44,0:44:99:0,120,1800:0,120,1800 0/0:51,0:51:99:0,110,1358:0,110,1358 0/1:32,46:78:99:934,0,618:934,0,618
5 41862758 rs75134564 G A 1221.18 PASS AF=0.063;FS=0.000;MQ=60.00;QD=12.72;VQSLOD=5.85;CLNDBN=Succinyl-CoA_acetoacetate_transferase_deficiency;CLNREVSTAT=no_criteria;CLNSIG=5;OM;PM;X1000Gp3_AF=0.00159744;ExAC_AF=1.334e-03;ESP6500_AF=7.68876e-05;BIOBANK_AF_v20171101=9.524e-04;dbNSFP_PROVEAN_pred=N;dbNSFP_Polyphen2_HVAR_pred=P;dbNSFP_SIFT_pred=D;ANN=A|missense_variant|MODERATE|OXCT1|OXCT1|transcript|NM_000436|protein_coding|2/17|c.173C>T|p.Thr58Met|504/3558|173/1563|58/520|| GT:AD:DP:GQ:PL:PP 0/0:57,0:57:99:0,99,1485:0,123,1539 0/0:69,0:69:99:0,120,1800:0,144,1854 0/0:63,0:63:99:0,120,1800:0,144,1854 0/1:35,61:96:99:1264,0,572:1240,0,602 0/0:79,0:79:99:0,120,1800:0,144,1854 0/0:59,0:59:99:0,99,1485:0,123,1539 0/0:53,0:53:99:0,102,1530:0,126,1584 0/0:49,0:49:99:0,111,1134:0,135,1188
6 157519969 rs748363079 T C 488.18 PASS AF=0.063;FS=0.000;MQ=60.00;QD=5.88;VQSLOD=7.73;CLNDBN=Coffin-Siris_syndrome_1;CLNREVSTAT=no_criteria;CLNSIG=5;PM;ExAC_AF=5.767e-05;ANN=C|synonymous_variant|LOW|ARID1B|ARID1B|transcript|NM_020732|protein_coding|17/20|c.4038T>C|p.Tyr1346Tyr|4038/9638|4038/6750|1346/2249||,C|synonymous_variant|LOW|ARID1B|ARID1B|transcript|NM_017519|protein_coding|16/19|c.3999T>C|p.Tyr1333Tyr|3999/9599|3999/6711|1333/2236|| GT:AD:DP:GQ:PL:PP 0/0:44,0:44:99:0,111,1665:0,111,1665 0/0:38,0:38:99:0,99,1485:0,99,1485 0/0:46,0:46:99:0,120,1800:0,120,1800 0/1:52,31:83:99:531,0,1082:531,0,1082 0/0:64,0:64:99:0,120,1800:0,120,1800 0/0:45,0:45:99:0,117,1755:0,117,1755 0/0:46,0:46:99:0,117,1160:0,117,1160 0/0:43,0:43:99:0,102,1530:0,102,1530
15 28228553 rs74653330 C T 18183.82 PASS AF=0.063;FS=4.082;MQ=60.00;QD=11.69;VQSLOD=6.58;CLNDBN=Tyrosinase-positive_oculocutaneous_albinism|not_specified|not_provided;CLNREVSTAT=no_criteria|mult|single;CLNSIG=5|3|0;OM;PM;X1000Gp3_AF=0.00798722;ExAC_AF=7.750e-03;ESP6500_AF=0.00130709;BIOBANK_AF_v20171101=0.018;dbNSFP_PROVEAN_pred=N,N,D;dbNSFP_Polyphen2_HVAR_pred=P,P;dbNSFP_SIFT_pred=T,T,T;ANN=T|missense_variant|MODERATE|OCA2|OCA2|transcript|NM_000275|protein_coding|14/24|c.1441G>A|p.Ala481Thr|1551/3138|1441/2517|481/838||,T|missense_variant|MODERATE|OCA2|OCA2|transcript|NM_001300984|protein_coding|13/23|c.1369G>A|p.Ala457Thr|1479/3068|1369/2445|457/814|| GT:AD:DP:GQ:PL:PP 0/0:39,0:39:99:0,100,1178:0,118,1220 0/0:40,0:40:99:0,99,1485:0,117,1527 0/0:41,0:41:99:0,99,1164:0,117,1206 0/0:34,0:34:99:0,102,865:0,120,907 0/1:45,30:75:99:594,0,1031:576,0,1055 0/0:34,0:34:99:0,99,956:0,117,998 0/0:35,0:35:99:0,105,948:0,123,990 0/0:36,0:36:99:0,105,972:0,123,1014
15 80472526 rs11555096 C T 18199.02 PASS AF=0.063;FS=1.088;MQ=60.00;QD=11.69;VQSLOD=12.74;CLNDBN=Fumarylacetoacetase_pseudodeficiency|Tyrosinemia_type_I|not_provided;CLNREVSTAT=no_criteria|no_criteria|single;CLNSIG=5|5|255;OM;PM;X1000Gp3_AF=0.00798722;ExAC_AF=0.017;ESP6500_AF=0.0163002;BIOBANK_AF_v20171101=0.047;dbNSFP_PROVEAN_pred=D,D,D;dbNSFP_Polyphen2_HVAR_pred=D;dbNSFP_SIFT_pred=D,D,D;ANN=T|missense_variant|MODERATE|FAH|FAH|transcript|NM_000137|protein_coding|12/14|c.1021C>T|p.Arg341Trp|1185/1797|1021/1260|341/419|| GT:AD:DP:GQ:PL:PP 0/0:35,0:35:99:0,102,941:0,120,983 0/0:35,0:35:99:0,105,961:0,123,1003 0/0:40,0:40:99:0,99,1485:0,117,1527 0/0:35,0:35:99:0,99,950:0,117,992 0/0:37,0:37:99:0,102,979:0,120,1021 0/1:33,28:61:99:579,0,768:561,0,792 0/0:46,0:46:99:0,120,1800:0,138,1842 0/0:37,0:37:99:0,99,968:0,117,1010
16 2168022 rs199476099 C A 5772.61 PASS AF=0.063;FS=2.472;MQ=40.41;QD=10.67;VQSLOD=-4.142e+00;CLNDBN=Polycystic_kidney_disease\x2c_adult_type;CLNREVSTAT=no_criteria;CLNSIG=5;OM;PM;X1000Gp3_AF=0.000998403;ExAC_AF=2.248e-03;ESP6500_AF=0.00160973;BIOBANK_AF_v20171101=0.021;dbNSFP_PROVEAN_pred=N,N,N;dbNSFP_Polyphen2_HVAR_pred=B,P;dbNSFP_SIFT_pred=T,T,D;ANN=A|missense_variant|MODERATE|PKD1|PKD1|transcript|NM_001009944|protein_coding|5/46|c.971G>T|p.Arg324Leu|1180/14138|971/12912|324/4303||,A|missense_variant|MODERATE|PKD1|PKD1|transcript|NM_000296|protein_coding|5/46|c.971G>T|p.Arg324Leu|1180/14135|971/12909|324/4302|| GT:AD:DP:GQ:PL:PP 0/1:36,16:52:99:272,0,805:246,0,837 0/0:47,0:47:99:0,120,1800:0,146,1858 0/0:36,0:36:99:0,99,1203:0,125,1261 0/0:34,0:34:99:0,99,1132:0,125,1190 0/0:33,0:33:99:0,99,1040:0,125,1098 0/0:37,0:37:99:0,102,1530:0,128,1588 0/0:44,0:44:99:0,101,1350:0,127,1408 0/0:42,0:42:99:0,120,1800:0,146,1858
16 14041848 rs121913049 C T 1448.57 PASS AF=0.063;FS=3.883;MQ=60.00;QD=9.92;VQSLOD=4.35;CLNDBN=Xeroderma_pigmentosum\x2c_group_F|not_specified|not_provided|Cockayne_syndrome|Fanconi_anemia\x2c_complementation_group_Q|Xeroderma_pigmentosum\x2c_group_F;CLNREVSTAT=no_criteria|single|single|single|single|single;CLNSIG=5|0|0|0|0|0;OM;PM;ExAC_AF=5.107e-04;ESP6500_AF=0.000769586;BIOBANK_AF_v20171101=2.846e-03;dbNSFP_PROVEAN_pred=D,D;dbNSFP_Polyphen2_HVAR_pred=D;dbNSFP_SIFT_pred=D,D;ANN=T|missense_variant|MODERATE|ERCC4|ERCC4|transcript|NM_005236|protein_coding|11/11|c.2395C>T|p.Arg799Trp|2404/6761|2395/2751|799/916|| GT:AD:DP:GQ:PL:PP 0/0:36,0:36:99:0,99,987:0,99,987 0/0:36,0:36:99:0,108,960:0,108,960 0/0:35,0:35:99:0,99,1451:0,99,1451 0/0:40,0:40:99:0,99,1485:0,99,1485 0/0:34,0:34:99:0,99,919:0,99,919 0/1:43,25:68:99:476,0,957:476,0,957 0/0:40,0:40:99:0,102,1139:0,102,1139 0/0:36,0:36:99:0,99,1220:0,99,1220
16 66551110 rs137886900 G A 2803.57 PASS AF=0.063;FS=1.769;MQ=60.00;QD=14.23;VQSLOD=7.29;CLNDBN=Mitochondrial_DNA_depletion_syndrome_2|Progressive_external_ophthalmoplegia_with_mitochondrial_DNA_deletions\x2c_autosomal_recessive_3,Mitochondrial_DNA_depletion_syndrome_2;CLNREVSTAT=no_criteria|no_criteria,no_criteria;CLNSIG=5|5,5;OM;PM;ExAC_AF=9.060e-05;BIOBANK_AF_v20171101=9.560e-04;dbNSFP_PROVEAN_pred=D,D,D,D,D,D,D,D;dbNSFP_Polyphen2_HVAR_pred=D,D,D,D,D;dbNSFP_SIFT_pred=D,D,D,D,D,D,D,D;ANN=A|missense_variant|MODERATE|TK2|TK2|transcript|NM_004614|protein_coding|8/10|c.547C>T|p.Arg183Trp|898/5114|547/798|183/265||,A|missense_variant|MODERATE|TK2|TK2|transcript|NM_001272050|protein_coding|8/10|c.256C>T|p.Arg86Trp|672/4888|256/507|86/168||,A|missense_variant|MODERATE|TK2|TK2|transcript|NM_001172643|protein_coding|8/10|c.454C>T|p.Arg152Trp|462/4678|454/705|152/234||,A|missense_variant|MODERATE|TK2|TK2|transcript|NM_001172644|protein_coding|7/9|c.472C>T|p.Arg158Trp|823/5039|472/723|158/240||,A|missense_variant|MODERATE|TK2|TK2|transcript|NM_001172645|protein_coding|7/9|c.493C>T|p.Arg165Trp|844/5060|493/744|165/247||,A|missense_variant|MODERATE|TK2|TK2|transcript|NM_001271934|protein_coding|9/11|c.400C>T|p.Arg134Trp|993/5209|400/651|134/216||,A|intron_variant|MODIFIER|TK2|TK2|transcript|NM_001271935|protein_coding|6/7|c.357-3396C>T||||||,A|non_coding_exon_variant|MODIFIER|TK2|TK2|transcript|NR_073520|pseudogene|7/9|n.1826C>T|||||| GT:AD:DP:GQ:PL:PP 0/0:34,0:34:99:0,102,852:0,136,923 0/0:38,0:38:99:0,106,966:0,140,1037 0/0:38,0:38:99:0,111,1665:0,145,1736 0/0:34,0:34:99:0,99,853:0,133,924 0/0:36,0:36:99:0,105,1034:0,139,1105 0/1:19,34:53:99:750,0,325:716,0,362 0/0:36,0:36:99:0,102,1034:0,136,1105 0/0:34,0:34:99:0,102,867:0,136,938
17 12899902 rs5030739 C T 12571.79 PASS AF=0.063;FS=1.105;MQ=60.00;QD=11.08;VQSLOD=13.08;CLNDBN=Prostate_cancer\x2c_hereditary\x2c_2|not_specified|Combined_oxidative_phosphorylation_deficiency_17;CLNREVSTAT=no_criteria|mult|single;CLNSIG=5|2|2;OM;PM;X1000Gp3_AF=0.0231629;ExAC_AF=0.034;ESP6500_AF=0.028756;BIOBANK_AF_v20171101=0.030;dbNSFP_PROVEAN_pred=N,N,N,N;dbNSFP_Polyphen2_HVAR_pred=B,B,B,B,B,B,B,B;dbNSFP_SIFT_pred=T,T,T,T;ANN=T|missense_variant|MODERATE|ELAC2|ELAC2|transcript|NM_018127|protein_coding|17/24|c.1621G>A|p.Ala541Thr|1738/3804|1621/2481|541/826||,T|missense_variant|MODERATE|ELAC2|ELAC2|transcript|NM_001165962|protein_coding|16/23|c.1501G>A|p.Ala501Thr|1618/3684|1501/2361|501/786||,T|missense_variant|MODERATE|ELAC2|ELAC2|transcript|NM_173717|protein_coding|17/24|c.1618G>A|p.Ala540Thr|1735/3801|1618/2478|540/825||,T|downstream_gene_variant|MODIFIER|ARHGAP44|ARHGAP44|transcript|NM_014859|protein_coding||c.*6414C>T|||||4941|,T|downstream_gene_variant|MODIFIER|ARHGAP44|ARHGAP44|transcript|NM_001321164|protein_coding||c.*9477C>T|||||4941|,T|downstream_gene_variant|MODIFIER|ARHGAP44|ARHGAP44|transcript|NM_001321166|protein_coding||c.*6414C>T|||||4941|,T|downstream_gene_variant|MODIFIER|ARHGAP44|ARHGAP44|transcript|NM_001321167|protein_coding||c.*9477C>T|||||4941|,T|downstream_gene_variant|MODIFIER|ARHGAP44|ARHGAP44|transcript|NM_001321168|protein_coding||c.*9477C>T|||||4941|,T|downstream_gene_variant|MODIFIER|ARHGAP44|ARHGAP44|transcript|NR_135569|pseudogene||n.*4941C>T|||||4941| GT:AD:DP:GQ:PL:PP 0/0:59,0:59:99:0,120,1800:0,133,1832 0/0:88,0:88:99:0,120,1800:0,133,1832 0/0:78,0:78:99:0,120,1800:0,133,1832 0/0:37,0:37:99:0,102,1530:0,115,1562 0/1:68,37:105:99:730,0,1603:717,0,1622 0/0:77,0:77:99:0,120,1800:0,133,1832 0/0:78,0:78:99:0,120,1800:0,133,1832 0/0:68,0:68:99:0,120,1800:0,133,1832
17 72759575 rs119486097 G A 5172.58 PASS AF=0.063;FS=0.000;MQ=60.00;QD=10.94;VQSLOD=7.40;CLNDBN=Nephrolithiasis/osteoporosis\x2c_hypophosphatemic\x2c_2|not_specified;CLNREVSTAT=no_criteria|single;CLNSIG=5|3;OM;PM;X1000Gp3_AF=0.000998403;ESP6500_AF=0.00238352;BIOBANK_AF_v20171101=0.010;dbNSFP_PROVEAN_pred=D,N;dbNSFP_Polyphen2_HVAR_pred=P,.;dbNSFP_SIFT_pred=D,T;ANN=A|missense_variant|MODERATE|SLC9A3R1|SLC9A3R1|transcript|NM_004252|protein_coding|3/6|c.673G>A|p.Glu225Lys|908/2016|673/1077|225/358|| GT:AD:DP:GQ:PL:PP 0/0:53,0:53:99:0,120,1800:0,146,1858 0/0:91,0:91:99:0,120,1800:0,146,1858 0/1:95,68:163:99:1404,0,1936:1378,0,1968 0/0:55,0:55:99:0,120,1800:0,146,1858 0/0:101,0:101:99:0,120,1800:0,146,1858 0/0:69,0:69:99:0,120,1800:0,146,1858 0/0:74,0:74:99:0,120,1800:0,146,1858 0/0:47,0:47:99:0,115,1369:0,141,1427
18 57134052 rs121908253 G A 703.18 PASS AF=0.063;FS=0.869;MQ=60.00;QD=9.25;VQSLOD=4.52;CLNDBN=Hennekam_lymphangiectasia-lymphedema_syndrome;CLNREVSTAT=no_criteria;CLNSIG=5;OM;PM;X1000Gp3_AF=0.000199681;ExAC_AF=2.224e-04;ESP6500_AF=0.000230663;dbNSFP_PROVEAN_pred=D;dbNSFP_Polyphen2_HVAR_pred=B;dbNSFP_SIFT_pred=D;ANN=A|missense_variant|MODERATE|CCBE1|CCBE1|transcript|NM_133459|protein_coding|5/11|c.472C>T|p.Arg158Cys|542/6260|472/1221|158/406|| GT:AD:DP:GQ:PL:PP 0/0:39,0:39:99:0,111,1665:0,142,1731 0/0:46,0:46:99:0,99,1485:0,130,1551 0/0:40,0:40:99:0,105,1575:0,136,1641 0/1:37,39:76:99:746,0,703:715,0,738 0/0:48,0:48:99:0,117,1755:0,148,1821 0/0:43,0:43:99:0,99,1485:0,130,1551 0/0:39,0:39:99:0,101,1307:0,132,1373 0/0:41,0:41:99:0,105,1575:0,136,1641
19 11210912 rs2228671 C T 46978.43 PASS AF=0.063;FS=0.000;MQ=60.00;QD=12.25;VQSLOD=13.74;CLNDBN=Familial_hypercholesterolemia,Familial_hypercholesterolemia,Familial_hypercholesterolemia|not_specified;CLNREVSTAT=mult,conf,conf|mult;CLNSIG=5,255,255|2;OM;PM;X1000Gp3_AF=0.0569089;ExAC_AF=0.086;ESP6500_AF=0.0905736;BIOBANK_AF_v20171101=0.083;ANN=T|synonymous_variant|LOW|LDLR|LDLR|transcript|NM_000527|protein_coding|2/18|c.81C>T|p.Cys27Cys|268/5283|81/2583|27/860||,T|synonymous_variant|LOW|LDLR|LDLR|transcript|NM_001195798|protein_coding|2/18|c.81C>T|p.Cys27Cys|268/5277|81/2577|27/858||,T|synonymous_variant|LOW|LDLR|LDLR|transcript|NM_001195799|protein_coding|2/17|c.81C>T|p.Cys27Cys|268/5160|81/2460|27/819||,T|synonymous_variant|LOW|LDLR|LDLR|transcript|NM_001195800|protein_coding|2/16|c.81C>T|p.Cys27Cys|268/4779|81/2079|27/692||,T|synonymous_variant|LOW|LDLR|LDLR|transcript|NM_001195803|protein_coding|2/16|c.81C>T|p.Cys27Cys|268/4749|81/2049|27/682|| GT:AD:DP:GQ:PL:PP 0/1:55,43:98:99:815,0,1150:806,0,1165 0/0:50,0:50:99:0,117,1755:0,126,1779 0/0:51,0:51:99:0,120,1800:0,129,1824 0/0:39,0:39:99:0,102,1530:0,111,1554 0/0:63,0:63:99:0,120,1800:0,129,1824 0/0:45,0:45:99:0,99,1485:0,108,1509 0/0:42,0:42:99:0,120,1800:0,129,1824 0/0:48,0:48:99:0,99,1485:0,108,1509
19 35786868 rs2301600 C T 15890.4 PASS AF=0.188;FS=0.534;MQ=59.80;QD=13.39;VQSLOD=3.20;CLNDBN=Spastic_paraplegia_75\x2c_autosomal_recessive;CLNREVSTAT=no_criteria;CLNSIG=5;PM;X1000Gp3_AF=0.289537;ExAC_AF=0.263;ESP6500_AF=0.182741;BIOBANK_AF_v20171101=0.175;ANN=T|synonymous_variant|LOW|MAG|MAG|transcript|NM_002361|protein_coding|4/11|c.399C>T|p.Ser133Ser|597/2431|399/1881|133/626||,T|synonymous_variant|LOW|MAG|MAG|transcript|NM_001199216|protein_coding|4/11|c.324C>T|p.Ser108Ser|584/2418|324/1806|108/601||,T|synonymous_variant|LOW|MAG|MAG|transcript|NM_080600|protein_coding|4/12|c.399C>T|p.Ser133Ser|597/2476|399/1749|133/582|| GT:AD:DP:GQ:PL:PP 0/1:48,57:105:99:1170,0,902:1169,0,909 0/0:34,0:34:99:0,99,1081:0,100,1089 0/0:35,0:35:99:0,100,982:0,101,990 0/1:53,60:113:99:1241,0,999:1240,0,1006 0/0:33,0:33:99:0,99,1051:0,100,1059 0/0:53,0:53:99:0,120,1800:0,121,1808 0/1:46,43:89:99:857,0,1043:856,0,1050 0/0:37,0:37:99:0,99,1485:0,100,1493
19 45316804 rs3810141 C T 14862.36 PASS AF=0.188;FS=0.523;MQ=60.00;QD=16.77;VQSLOD=9.05;CLNDBN=BLOOD_GROUP--LUTHERAN_NULL;CLNREVSTAT=no_criteria;CLNSIG=5;OM;PM;X1000Gp3_AF=0.10004;ExAC_AF=0.086;ESP6500_AF=0.0713736;BIOBANK_AF_v20171101=0.070;ANN=T|synonymous_variant|LOW|BCAM|BCAM|transcript|NM_005581|protein_coding|6/15|c.711C>T|p.Cys237Cys|777/2453|711/1887|237/628||,T|synonymous_variant|LOW|BCAM|BCAM|transcript|NM_001013257|protein_coding|6/14|c.711C>T|p.Cys237Cys|777/3431|711/1767|237/588|| GT:AD:DP:GQ:PGT:PID:PL:PP 0/0:34,0:34:99:.:.:0,102,901:0,109,920 0/0:34,0:34:99:.:.:0,99,957:0,106,976 0/1:23,33:56:99:0|1:45316804_C_T:1313,0,1047:1306,0,1060 0/0:34,0:34:99:.:.:0,102,908:0,109,927 0/1:45,36:81:99:0|1:45316804_C_T:1376,0,2228:1369,0,2241 0/0:39,0:39:99:.:.:0,101,1068:0,108,1087 0/1:25,28:53:99:0|1:45316804_C_T:1112,0,1172:1105,0,1185 0/0:45,0:45:99:.:.:0,109,1237:0,116,1256
20 5283323 rs74315416 A C 586.18 PASS AF=0.063;FS=0.000;MQ=60.00;QD=7.92;VQSLOD=4.24;CLNDBN=Kallmann_syndrome_3|not_specified|Hypogonadism_with_anosmia;CLNREVSTAT=no_criteria|single|single;CLNSIG=5|3|3;OM;PM;X1000Gp3_AF=0.000998403;ExAC_AF=2.249e-03;ESP6500_AF=0.00261418;dbNSFP_PROVEAN_pred=D,D;dbNSFP_Polyphen2_HVAR_pred=D;dbNSFP_SIFT_pred=D,D;ANN=C|missense_variant|MODERATE|PROKR2|PROKR2|transcript|NM_144773|protein_coding|3/3|c.518T>G|p.Leu173Arg|765/2242|518/1155|173/384|| GT:AD:DP:GQ:PL:PP 0/0:46,0:46:99:0,120,1800:0,146,1858 0/0:80,0:80:99:0,120,1800:0,146,1858 0/0:77,0:77:99:0,120,1800:0,146,1858 0/0:56,0:56:99:0,120,1800:0,146,1858 0/0:58,0:58:99:0,120,1800:0,146,1858 0/0:77,0:77:99:0,120,1800:0,146,1858 0/0:46,0:46:99:0,120,1800:0,146,1858 0/1:42,32:74:99:629,0,856:603,0,888
20 5283323 rs74315416 A C 586.18 PASS AF=0.063;FS=0.000;MQ=60.00;QD=7.92;VQSLOD=4.24;CLNDBN=Kallmann_syndrome_3|not_specified|Hypogonadism_with_anosmia;CLNREVSTAT=no_criteria|single|single;CLNSIG=5|3|3;OM;PM;X1000Gp3_AF=0.000998403;ExAC_AF=2.249e-03;ESP6500_AF=0.00261418;dbNSFP_PROVEAN_pred=D,D;dbNSFP_Polyphen2_HVAR_pred=D;dbNSFP_SIFT_pred=D,D;ANN=C|missense_variant|MODERATE|PROKR2|PROKR2|transcript|NM_144773|protein_coding|3/3|c.518T>G|p.Leu173Arg|765/2242|518/1155|173/384|| GT:AD:DP:GQ:PL:PP 0/0:46,0:46:99:0,120,1800:0,146,1858 0/0:80,0:80:99:0,120,1800:0,146,1858 0/0:77,0:77:99:0,120,1800:0,146,1858 0/0:56,0:56:99:0,120,1800:0,146,1858 0/0:58,0:58:99:0,120,1800:0,146,1858 0/0:77,0:77:99:0,120,1800:0,146,1858 0/0:46,0:46:99:0,120,1800:0,146,1858 0/1:42,32:74:99:629,0,856:603,0,888
20 23618427 rs1064039 C T 19026.03 PASS AF=0.063;FS=0.571;MQ=59.98;QD=12.43;VQSLOD=1.68;CLNDBN=Age-related_macular_degeneration_11;CLNREVSTAT=no_criteria;CLNSIG=5;OM;PM;X1000Gp3_AF=0.21226;ExAC_AF=0.120;ESP6500_AF=0.177988;BIOBANK_AF_v20171101=0.229;dbNSFP_PROVEAN_pred=N,N,N;dbNSFP_Polyphen2_HVAR_pred=B;dbNSFP_SIFT_pred=T,T,T;ANN=T|missense_variant|MODERATE|CST3|CST3|transcript|NM_000099|protein_coding|1/3|c.73G>A|p.Ala25Thr|259/886|73/441|25/146||,T|missense_variant|MODERATE|CST3|CST3|transcript|NM_001288614|protein_coding|1/4|c.73G>A|p.Ala25Thr|259/2198|73/441|25/146|| GT:AD:DP:GQ:PL:PP 0/0:50,0:50:99:0,110,1420:0,113,1431 0/0:42,0:42:99:0,111,1420:0,114,1431 0/0:37,0:37:99:0,105,1575:0,108,1586 0/1:45,40:85:99:822,0,934:819,0,943 0/0:39,0:39:99:0,102,1530:0,105,1541 0/0:39,0:39:99:0,102,1530:0,105,1541 0/0:44,0:44:99:0,111,1665:0,114,1676 0/0:42,0:42:99:0,99,1485:0,102,1496
20 43280227 rs73598374 C T 8472.7 PASS AF=0.125;FS=0.521;MQ=60.00;QD=12.02;VQSLOD=9.49;CLNDBN=Adenosine_deaminase_2_allozyme|Severe_combined_immunodeficiency_due_to_ADA_deficiency;CLNREVSTAT=no_criteria|single;CLNSIG=5|3;OM;PM;X1000Gp3_AF=0.0513179;ExAC_AF=0.034;ESP6500_AF=0.0308014;BIOBANK_AF_v20171101=0.049;dbNSFP_PROVEAN_pred=N,N;dbNSFP_Polyphen2_HVAR_pred=B;dbNSFP_SIFT_pred=T,T;ANN=T|missense_variant|MODERATE|ADA|ADA|transcript|NM_000022|protein_coding|1/12|c.22G>A|p.Asp8Asn|173/1558|22/1092|8/363||,T|missense_variant|MODERATE|ADA|ADA|transcript|NM_001322051|protein_coding|1/11|c.22G>A|p.Asp8Asn|173/1486|22/1020|8/339||,T|5_prime_UTR_variant|MODIFIER|ADA|ADA|transcript|NM_001322050|protein_coding|1/11|c.-268G>A|||||25058|,T|downstream_gene_variant|MODIFIER|LINC01260|LINC01260|transcript|NR_034104|pseudogene||n.*4865G>A|||||4865|,T|non_coding_exon_variant|MODIFIER|ADA|ADA|transcript|NR_136160|pseudogene|1/11|n.173G>A|||||| GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:28,17:45:99:.:.:335,0,581:325,0,597 0/0:34,0:34:99:.:.:0,102,884:0,112,909 0/0:35,0:35:99:.:.:0,102,1530:0,112,1555 0/0:35,0:35:99:.:.:0,102,918:0,112,943 0/0:43,0:43:99:.:.:0,116,1173:0,126,1198 0/0:36,0:36:99:.:.:0,108,929:0,118,954 0/0:34,0:34:99:.:.:0,99,931:0,109,956 0/1:22,32:54:99:1|0:43280205_C_A:692,0,453:682,0,469
21 46931109 rs12483377 G A 26975.46 PASS AF=0.125;FS=0.523;MQ=60.23;QD=11.53;VQSLOD=2.34;CLNDBN=Knobloch_syndrome_1|not_specified;CLNREVSTAT=no_criteria|single;CLNSIG=5|2;OM;PM;X1000Gp3_AF=0.0443291;ExAC_AF=0.059;ESP6500_AF=0.0710223;BIOBANK_AF_v20171101=0.081;dbNSFP_PROVEAN_pred=D,D,D,D,D,D;dbNSFP_Polyphen2_HVAR_pred=D,D,D,D;dbNSFP_SIFT_pred=T,T,T,T,D,T;ANN=A|missense_variant|MODERATE|COL18A1|COL18A1|transcript|NM_130444|protein_coding|41/42|c.5014G>A|p.Asp1672Asn|5035/6599|5014/5256|1672/1751||,A|missense_variant|MODERATE|COL18A1|COL18A1|transcript|NM_130445|protein_coding|42/43|c.3769G>A|p.Asp1257Asn|3863/5427|3769/4011|1257/1336||,A|missense_variant|MODERATE|COL18A1|COL18A1|transcript|NM_030582|protein_coding|41/42|c.4309G>A|p.Asp1437Asn|4330/5894|4309/4551|1437/1516||,A|downstream_gene_variant|MODIFIER|SLC19A1|SLC19A1|transcript|NM_194255|protein_coding||c.*4463C>T|||||3520|,A|downstream_gene_variant|MODIFIER|SLC19A1|SLC19A1|transcript|NM_001205207|protein_coding||c.*4463C>T|||||3520|,A|downstream_gene_variant|MODIFIER|SLC19A1|SLC19A1|transcript|NM_001205206|protein_coding||c.*3781C>T|||||3520| GT:AD:DP:GQ:PL:PP 0/0:89,0:89:99:0,120,1800:0,130,1827 0/1:101,102:203:99:2009,0,2111:1999,0,2127 0/0:96,0:96:99:0,120,1800:0,130,1827 0/0:116,0:116:99:0,120,1800:0,130,1827 0/0:100,0:100:99:0,120,1800:0,130,1827 0/0:121,0:121:99:0,120,1800:0,130,1827 0/1:72,95:167:99:1974,0,1452:1964,0,1468 0/0:111,0:111:99:0,120,1800:0,130,1827
22 17670877 rs146597836 C T 924.18 PASS AF=0.063;FS=3.649;MQ=60.00;QD=9.24;VQSLOD=5.13;CLNDBN=Behcet's_syndrome;CLNREVSTAT=no_criteria;CLNSIG=5;X1000Gp3_AF=0.000599042;ExAC_AF=1.977e-03;ESP6500_AF=0.00161464;dbNSFP_PROVEAN_pred=N,N,N,N,N;dbNSFP_Polyphen2_HVAR_pred=B,B;dbNSFP_SIFT_pred=T,T,T,T,T;ANN=T|missense_variant|MODERATE|CECR1|CECR1|transcript|NM_001282225|protein_coding|6/10|c.927G>A|p.Met309Ile|1203/4505|927/1536|309/511||,T|missense_variant|MODERATE|CECR1|CECR1|transcript|NM_177405|protein_coding|3/7|c.204G>A|p.Met68Ile|409/3711|204/813|68/270||,T|missense_variant|MODERATE|CECR1|CECR1|transcript|NM_001282226|protein_coding|6/10|c.927G>A|p.Met309Ile|1170/4472|927/1536|309/511||,T|missense_variant|MODERATE|CECR1|CECR1|transcript|NM_001282228|protein_coding|6/10|c.801G>A|p.Met267Ile|1078/4380|801/1410|267/469||,T|missense_variant|MODERATE|CECR1|CECR1|transcript|NM_001282229|protein_coding|5/9|c.567G>A|p.Met189Ile|835/4137|567/1176|189/391||,T|missense_variant|MODERATE|CECR1|CECR1|transcript|NM_001282227|protein_coding|6/10|c.801G>A|p.Met267Ile|976/4278|801/1410|267/469|| GT:AD:DP:GQ:PL:PP 0/0:43,0:43:99:0,120,1800:0,148,1861 0/0:60,0:60:99:0,120,1800:0,148,1861 0/0:61,0:61:99:0,120,1800:0,148,1861 0/0:51,0:51:99:0,120,1800:0,148,1861 0/0:54,0:54:99:0,120,1800:0,148,1861 0/0:61,0:61:99:0,120,1800:0,148,1861 0/1:54,46:100:99:967,0,1205:939,0,1238 0/0:62,0:62:99:0,120,1800:0,148,1861
22 18901004 rs450046 C T 391886.21 PASS AF=1.00;FS=0.000;MQ=59.93;QD=28.11;VQSLOD=1.91;CLNDBN=Proline_dehydrogenase_deficiency|Schizophrenia_4|not_provided;CLNREVSTAT=no_criteria|no_criteria|no_criteria;CLNSIG=5|255|5;OM;PM;X1000Gp3_AF=0.905551;ExAC_AF=0.915;ESP6500_AF=0.904201;BIOBANK_AF_v20171101=0.912;dbNSFP_PROVEAN_pred=N,N;dbNSFP_Polyphen2_HVAR_pred=B;dbNSFP_SIFT_pred=T,T;ANN=T|missense_variant|MODERATE|PRODH|PRODH|transcript|NM_016335|protein_coding|14/15|c.1562G>A|p.Arg521Gln|1766/2408|1562/1803|521/600||,T|missense_variant|MODERATE|PRODH|PRODH|transcript|NM_001195226|protein_coding|13/14|c.1238G>A|p.Arg413Gln|1351/1993|1238/1479|413/492||,T|downstream_gene_variant|MODIFIER|DGCR6|DGCR6|transcript|NM_005675|protein_coding||c.*1802C>T|||||1403| GT:AD:DP:GQ:PL:PP 1/1:0,104:104:99:2711,311,0:2731,318,0 1/1:2,165:167:99:4575,451,0:4595,458,0 1/1:0,172:172:99:4712,515,0:4732,522,0 1/1:0,121:121:99:3226,362,0:3246,369,0 1/1:0,151:151:99:4435,453,0:4455,460,0 1/1:0,109:109:99:2888,325,0:2908,332,0 1/1:0,132:132:99:3675,398,0:3695,405,0 1/1:0,129:129:99:3484,385,0:3504,392,0
22 18905964 rs2904552 C T 11385.86 PASS AF=0.125;FS=1.120;MQ=55.19;NEGATIVE_TRAIN_SITE;QD=13.41;VQSLOD=-1.877e+00;CLNDBN=Proline_dehydrogenase_deficiency|Schizophrenia_4;CLNREVSTAT=no_criteria|no_criteria;CLNSIG=5|255;OM;PM;X1000Gp3_AF=0.0429313;ExAC_AF=0.075;ESP6500_AF=0.0815903;BIOBANK_AF_v20171101=0.068;dbNSFP_PROVEAN_pred=D,D;dbNSFP_Polyphen2_HVAR_pred=B,P,B;dbNSFP_SIFT_pred=D,T;ANN=T|missense_variant|MODERATE|PRODH|PRODH|transcript|NM_016335|protein_coding|12/15|c.1292G>A|p.Arg431His|1496/2408|1292/1803|431/600||,T|missense_variant|MODERATE|PRODH|PRODH|transcript|NM_001195226|protein_coding|11/14|c.968G>A|p.Arg323His|1081/1993|968/1479|323/492|| GT:AD:DP:GQ:PL:PP 0/0:40,0:40:99:0,111,1665:0,121,1692 0/0:65,0:65:99:0,120,1800:0,130,1827 0/0:73,0:73:99:0,120,1800:0,130,1827 0/0:44,0:44:99:0,120,1800:0,130,1827 0/0:54,0:54:99:0,120,1800:0,130,1827 1/1:0,99:99:99:2675,297,0:2648,281,0 0/0:71,0:71:99:0,120,1800:0,130,1827 0/0:59,0:59:99:0,118,1424:0,128,1451
22 24896073 rs138081800 A G 726.18 PASS AF=0.063;FS=2.128;MQ=60.00;QD=11.00;VQSLOD=5.33;CLNDBN=Deficiency_of_beta-ureidopropionase;CLNREVSTAT=no_criteria;CLNSIG=5;PM;ExAC_AF=4.365e-04;ESP6500_AF=0.000153775;ANN=G|splice_acceptor_variant&intron_variant|HIGH|UPB1|UPB1|transcript|NM_016327|protein_coding|1/9|c.105-2A>G||||||;LOF=(UPB1|UPB1|1|1.00) GT:AD:DP:GQ:PL:PP 0/0:45,0:45:99:0,120,1800:0,120,1800 0/0:64,0:64:99:0,120,1800:0,120,1800 0/0:54,0:54:99:0,120,1800:0,120,1800 0/0:34,0:34:99:0,102,959:0,102,959 0/0:51,0:51:99:0,120,1800:0,120,1800 0/1:29,37:66:99:769,0,664:769,0,664 0/0:62,0:62:99:0,120,1800:0,120,1800 0/0:47,0:47:99:0,120,1800:0,120,1800
22 51063477 rs6151429 T C 1312.66 PASS AF=0.063;FS=0.726;MQ=60.00;QD=12.27;VQSLOD=12.48;CLNDBN=Arylsulfatase_A_pseudodeficiency|Metachromatic_leukodystrophy|not_provided|not_specified;CLNREVSTAT=no_criteria|conf|mult|single;CLNSIG=5|255|255|2;OM;PM;X1000Gp3_AF=0.0499201;BIOBANK_AF_v20171101=0.043;ANN=C|3_prime_UTR_variant|MODIFIER|ARSA|ARSA|transcript|NM_000487|protein_coding|8/8|c.*96A>G|||||96|,C|3_prime_UTR_variant|MODIFIER|ARSA|ARSA|transcript|NM_001085425|protein_coding|9/9|c.*96A>G|||||96|,C|3_prime_UTR_variant|MODIFIER|ARSA|ARSA|transcript|NM_001085426|protein_coding|9/9|c.*96A>G|||||96|,C|3_prime_UTR_variant|MODIFIER|ARSA|ARSA|transcript|NM_001085427|protein_coding|9/9|c.*96A>G|||||96|,C|3_prime_UTR_variant|MODIFIER|ARSA|ARSA|transcript|NM_001085428|protein_coding|8/8|c.*96A>G|||||96| GT:AD:DP:GQ:PL:PP 0/0:35,0:35:99:0,102,903:0,112,929 0/0:34,0:34:99:0,99,941:0,109,967 0/0:41,0:41:99:0,120,1800:0,130,1826 0/0:27,0:27:85:0,75,1125:0,85,1151 0/0:35,0:35:99:0,105,1009:0,115,1035 0/1:36,26:62:99:562,0,764:552,0,780 0/0:36,0:36:99:0,108,1023:0,118,1049 0/0:34,0:34:99:0,102,870:0,112,896
X 55057617 rs140772352 G C 8342.57 PASS AF=0.063;FS=0.000;MQ=60.00;QD=11.15;VQSLOD=6.81;CLNDBN=Hereditary_sideroblastic_anemia|not_specified;CLNREVSTAT=no_criteria|single;CLNSIG=5|0;PM;BIOBANK_AF_v20171101=0.010;ANN=C|upstream_gene_variant|MODIFIER|ALAS2|ALAS2|transcript|NM_000032|protein_coding||c.-5184C>G|||||120|,C|upstream_gene_variant|MODIFIER|ALAS2|ALAS2|transcript|NM_001037967|protein_coding||c.-5184C>G|||||120|,C|upstream_gene_variant|MODIFIER|ALAS2|ALAS2|transcript|NM_001037968|protein_coding||c.-3377C>G|||||120|,C|intergenic_region|MODIFIER|ALAS2-PAGE2B|ALAS2-PAGE2B|intergenic_region|ALAS2-PAGE2B|||n.55057617G>C|||||| GT:AD:DP:GQ:PL:PP 0/0:426,0:426:99:0,120,1800:0,120,1800 0/0:270,0:270:99:0,120,1800:0,120,1800 0/0:325,0:325:99:0,120,1800:0,120,1800 0/0:266,0:266:99:0,120,1800:0,120,1800 0/0:374,0:374:99:0,120,1800:0,120,1800 0/0:396,0:396:99:0,120,1800:0,120,1800 0/1:366,382:748:99:8380,0,7961:8380,0,7961 0/0:197,0:197:99:0,120,1800:0,120,1800
X 105278361 rs1804495 C A 22062.28 PASS AF=0.250;FS=0.000;MQ=60.00;QD=17.76;VQSLOD=11.81;CLNDBN=Thyroxine-binding_globulin\x2c_variant_P;CLNREVSTAT=no_criteria;CLNSIG=5;OM;PM;ExAC_AF=0.145;ESP6500_AF=0.115782;BIOBANK_AF_v20171101=0.080;dbNSFP_PROVEAN_pred=D,D;dbNSFP_Polyphen2_HVAR_pred=P;dbNSFP_SIFT_pred=D,D;ANN=A|missense_variant|MODERATE|SERPINA7|SERPINA7|transcript|NM_000354|protein_coding|4/5|c.909G>T|p.Leu303Phe|956/1596|909/1248|303/415|| GT:AD:DP:GQ:PL:PP 0/0:47,0:47:99:0,120,1800:0,120,1800 0/0:39,0:39:99:0,102,1530:0,102,1530 0/0:36,0:36:99:0,102,1033:0,102,1033 0/0:38,0:38:99:0,100,1189:0,100,1189 1/1:0,40:40:99:1066,119,0:1066,119,0 1/1:0,45:45:99:1225,135,0:1225,135,0 0/0:66,0:66:99:0,120,1800:0,120,1800 0/0:40,0:40:99:0,114,1710:0,114,1710