##fileformat=VCFv4.2
##ALT=<ID=*,Description="Represents allele(s) other than observed.">
##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
##FILTER=<ID=IndelGap,Description="Indel within 10 bp of an indel">
##FILTER=<ID=LOW_VQSLOD,Description="VQSLOD < 0.0">
##FILTER=<ID=LowQual,Description="Low quality">
##FILTER=<ID=PASS,Description="All filters passed">
##FILTER=<ID=SnpGap,Description="SNP within 3 bp of an indel">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
##FORMAT=<ID=CGT,Number=1,Type=Integer,Description="Constrained Genotype (0-based index to Number=G ordering).">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of high-quality non-reference bases">
##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=JL,Number=1,Type=Integer,Description="Phred-scaled joint likelihood of the genotype combination (before applying family priors)">
##FORMAT=<ID=JP,Number=1,Type=Integer,Description="Phred-scaled joint posterior probability of the genotype combination (after applying family priors)">
##FORMAT=<ID=MIN,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
##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=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
##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=RO,Number=1,Type=Integer,Description="Reference allele observation count">
##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
##FORMAT=<ID=UGT,Number=1,Type=Integer,Description="Unconstrained Genotype (0-based index to Number=G ordering).">
##GATKCommandLine.ApplyRecalibration=<ID=ApplyRecalibration,Version=3.6-0-g89b7209,Date="Thu Dec 08 17:57:26 CET 2016",Epoch=1481216246816,CommandLineOptions="analysis_type=ApplyRecalibration 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=/mnt/hds/proj/bioinfo/develop/references_4.0/Homo_sapiens.GRCh37.d5.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=[/mnt/hds/proj/bioinfo/develop/henrikS/internal_id/analysis/internal_id/internal_id.fam] pedigreeString=[] pedigreeValidationType=SILENT 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 input=[(RodBinding name=input source=/scratch/717408/internal_id_sorted_md_brecal_gvcf_BOTH.vcf)] recal_file=(RodBinding name=recal_file source=/scratch/717408/gatk/intermediary/internal_id_sorted_md_brecal_gvcf_BOTH.intervals) tranches_file=/scratch/717408/gatk/intermediary/internal_id_sorted_md_brecal_gvcf_BOTH.intervals.tranches out=/scratch/717408/internal_id_sorted_md_brecal_gvcf_vrecal_BOTH_filtered.vcf ts_filter_level=null useAlleleSpecificAnnotations=false lodCutoff=0.0 ignore_filter=null ignore_all_filters=false excludeFiltered=false mode=BOTH filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
##GATKCommandLine.CalculateGenotypePosteriors=<ID=CalculateGenotypePosteriors,Version=3.6-0-g89b7209,Date="Thu Dec 08 17:58:01 CET 2016",Epoch=1481216281078,CommandLineOptions="analysis_type=CalculateGenotypePosteriors 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=/mnt/hds/proj/bioinfo/develop/references_4.0/Homo_sapiens.GRCh37.d5.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=[/mnt/hds/proj/bioinfo/develop/henrikS/internal_id/analysis/internal_id/internal_id.fam] pedigreeString=[] pedigreeValidationType=SILENT 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=/scratch/717408/internal_id_sorted_md_brecal_gvcf_vrecal_BOTH.vcf) supporting=[(RodBinding name=supporting source=/mnt/hds/proj/bioinfo/develop/references_4.0/1000G_phase3_v4_20130502.sites.vcf)] globalPrior=0.001 deNovoPrior=1.0E-6 numRefSamplesIfNoCall=0 defaultToAC=false ignoreInputSamples=false discoveredACpriorsOff=false skipPopulationPriors=false skipFamilyPriors=false out=/scratch/717408/internal_id_sorted_md_brecal_gvcf_vrecal_BOTH_refined.vcf filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
##GATKCommandLine.CombineVariants=<ID=CombineVariants,Version=3.6-0-g89b7209,Date="Thu Dec 08 18:13:16 CET 2016",Epoch=1481217196258,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=/mnt/hds/proj/bioinfo/develop/references_4.0/Homo_sapiens.GRCh37.d5.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 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=[(RodBindingCollection [(RodBinding name=gatk source=/scratch/717409/internal_id_sorted_md_brecal_gvcf_vrecal_BOTH.vcf)]), (RodBindingCollection [(RodBinding name=freebayes source=/scratch/717409/internal_id_sorted_md_brecal_freebayes_BOTH.vcf)]), (RodBindingCollection [(RodBinding name=samtools source=/scratch/717409/internal_id_sorted_md_brecal_mpileup_BOTH.vcf)])] out=/scratch/717409/internal_id_sorted_md_brecal_gvcf_vrecal_comb_BOTH.vcf genotypemergeoption=PRIORITIZE filteredrecordsmergetype=KEEP_IF_ANY_UNFILTERED multipleallelesmergetype=BY_TYPE rod_priority_list=gatk,samtools,freebayes printComplexMerges=false filteredAreUncalled=false minimalVCF=false excludeNonVariants=true 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">
##GATKCommandLine.GenotypeGVCFs=<ID=GenotypeGVCFs,Version=3.6-0-g89b7209,Date="Thu Dec 08 17:38:06 CET 2016",Epoch=1481215086639,CommandLineOptions="analysis_type=GenotypeGVCFs input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[1] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/mnt/hds/proj/bioinfo/develop/references_4.0/Homo_sapiens.GRCh37.d5.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=16 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[/mnt/hds/proj/bioinfo/develop/henrikS/internal_id/analysis/internal_id/internal_id.fam] pedigreeString=[] pedigreeValidationType=SILENT 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=/mnt/hds/proj/bioinfo/develop/references_4.0/Merged_reference_infiles.gvcf)]), (RodBindingCollection [(RodBinding name=variant2 source=/scratch/717383/ADM1059A1_lanes_1_sorted_md_brecal_gvcf_1.vcf)]), (RodBindingCollection [(RodBinding name=variant3 source=/scratch/717383/ADM1059A2_lanes_1_sorted_md_brecal_gvcf_1.vcf)]), (RodBindingCollection [(RodBinding name=variant4 source=/scratch/717383/ADM1059A3_lanes_1_sorted_md_brecal_gvcf_1.vcf)])] out=/scratch/717383/internal_id_sorted_md_brecal_gvcf_BOTH_1.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 max_num_PL_values=100 input_prior=[] sample_ploidy=2 annotation=[] group=[StandardAnnotation] dbsnp=(RodBinding name=dbsnp source=/mnt/hds/proj/bioinfo/develop/references_4.0/dbsnp_138.b37.vcf) filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.6-0-g89b7209,Date="Thu Dec 08 17:33:37 CET 2016",Epoch=1481214817399,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/scratch/717380/ADM1059A1_lanes_1_sorted_md_brecal_1.bam] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[/scratch/717380/1_Agilent_SureSelectCRE.V1.GRCh37_targets.bed.pad100.interval_list] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/mnt/hds/proj/bioinfo/develop/references_4.0/Homo_sapiens.GRCh37.d5.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=[/mnt/hds/proj/bioinfo/develop/henrikS/internal_id/analysis/internal_id/internal_id.fam] pedigreeString=[] pedigreeValidationType=SILENT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=LINEAR variant_index_parameter=128000 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=dbsnp source=/mnt/hds/proj/bioinfo/develop/references_4.0/dbsnp_138.b37.vcf) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[BaseQualityRankSumTest, ChromosomeCounts, Coverage, DepthPerAlleleBySample, FisherStrand, MappingQualityRankSumTest, QualByDepth, RMSMappingQuality, ReadPosRankSumTest, StrandOddsRatio, 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 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 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=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=true 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.2=<ID=SelectVariants,Version=3.6-0-g89b7209,Date="Thu Dec 08 17:57:45 CET 2016",Epoch=1481216265990,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=/mnt/hds/proj/bioinfo/develop/references_4.0/Homo_sapiens.GRCh37.d5.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 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name= source=/scratch/717408/internal_id_sorted_md_brecal_gvcf_vrecal_BOTH_filtered.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/scratch/717408/internal_id_sorted_md_brecal_gvcf_vrecal_BOTH.vcf sample_name=[ADM1059A1, ADM1059A2, ADM1059A3] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[] 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 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">
##GATKCommandLine.SelectVariants=<ID=SelectVariants,Version=3.6-0-g89b7209,Date="Thu Dec 08 17:53:56 CET 2016",Epoch=1481216036265,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=/mnt/hds/proj/bioinfo/develop/references_4.0/Homo_sapiens.GRCh37.d5.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 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name= source=/scratch/717407/internal_id_sorted_md_brecal_gvcf_BOTH.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/scratch/717407/internal_id_sorted_md_brecal_gvcf_BOTH_incnonvariantloci.vcf sample_name=[ADM1059A1, ADM1059A2, ADM1059A3] 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">
##GATKCommandLine=<ID=CombineGVCFs,Version=3.1-1-g07a4bf8,Date="Thu Mar 27 11:31:13 CET 2014",Epoch=1395916273661,CommandLineOptions="analysis_type=CombineGVCFs input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=mip_references/Homo_sapiens.GRCh37.d5.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 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false 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 logging_level=INFO log_to_file=null help=false version=false variant=[(RodBindingCollection [(RodBinding name=variant source=/mnt/hds/proj/cust003/analysis/exomes/100-1-2A/mosaik/GATK/100-1-2A_lanes_5_sorted_pmd_rreal_brecal_gvcf.vcf)]), (RodBindingCollection [(RodBinding name=variant2 source=/mnt/hds/proj/cust003/analysis/exomes/100-1-4A/mosaik/GATK/100-1-4A_lanes_78_sorted_merged_pmd_rreal_brecal_gvcf.vcf)]), (RodBindingCollection [(RodBinding name=variant3 source=/mnt/hds/proj/cust003/analysis/exomes/100-2-1U/mosaik/GATK/100-2-1U_lanes_6_sorted_pmd_rreal_brecal_gvcf.vcf)]), (RodBindingCollection [(RodBinding name=variant4 source=/mnt/hds/proj/cust003/analysis/exomes/100-2-2U/mosaik/GATK/100-2-2U_lanes_6_sorted_pmd_rreal_brecal_gvcf.vcf)]), (RodBindingCollection [(RodBinding name=variant5 source=/mnt/hds/proj/cust003/analysis/exomes/120-1-1A/mosaik/GATK/120-1-1A_lanes_1122_sorted_merged_pmd_rreal_brecal_gvcf.vcf)]), (RodBindingCollection [(RodBinding name=variant6 source=/mnt/hds/proj/cust003/analysis/exomes/120-2-1U/mosaik/GATK/120-2-1U_lanes_1122_sorted_merged_pmd_rreal_brecal_gvcf.vcf)]), (RodBindingCollection [(RodBinding name=variant7 source=/mnt/hds/proj/cust003/analysis/exomes/120-2-2U/mosaik/GATK/120-2-2U_lanes_1122_sorted_merged_pmd_rreal_brecal_gvcf.vcf)]), (RodBindingCollection [(RodBinding name=variant8 source=/mnt/hds/proj/cust003/analysis/exomes/137-1-2A/mosaik/GATK/137-1-2A_lanes_111222_sorted_merged_pmd_rreal_brecal_gvcf.vcf)]), (RodBindingCollection [(RodBinding name=variant9 source=/mnt/hds/proj/cust003/analysis/exomes/142-1-1A/mosaik/GATK/142-1-1A_lanes_111222_sorted_merged_pmd_rreal_brecal_gvcf.vcf)]), (RodBindingCollection [(RodBinding name=variant10 source=/mnt/hds/proj/cust003/analysis/exomes/142-1-2A/mosaik/GATK/142-1-2A_lanes_111222_sorted_merged_pmd_rreal_brecal_gvcf.vcf)]), (RodBindingCollection [(RodBinding name=variant11 source=/mnt/hds/proj/cust003/analysis/exomes/142-2-1U/mosaik/GATK/142-2-1U_lanes_111222_sorted_merged_pmd_rreal_brecal_gvcf.vcf)]), (RodBindingCollection [(RodBinding name=variant12 source=/mnt/hds/proj/cust003/analysis/exomes/142-2-2U/mosaik/GATK/142-2-2U_lanes_111222_sorted_merged_pmd_rreal_brecal_gvcf.vcf)]), (RodBindingCollection [(RodBinding name=variant13 source=/mnt/hds/proj/cust003/analysis/exomes/143-1-1A/mosaik/GATK/143-1-1A_lanes_1122_sorted_merged_pmd_rreal_brecal_gvcf.vcf)]), (RodBindingCollection [(RodBinding name=variant14 source=/mnt/hds/proj/cust003/analysis/exomes/143-2-1U/mosaik/GATK/143-2-1U_lanes_1122_sorted_merged_pmd_rreal_brecal_gvcf.vcf)]), (RodBindingCollection [(RodBinding name=variant15 source=/mnt/hds/proj/cust003/analysis/exomes/143-2-2U/mosaik/GATK/143-2-2U_lanes_1122_sorted_merged_pmd_rreal_brecal_gvcf.vcf)]), (RodBindingCollection [(RodBinding name=variant16 source=/mnt/hds/proj/cust003/analysis/exomes/144-1-2A/mosaik/GATK/144-1-2A_lanes_111222_sorted_merged_pmd_rreal_brecal_gvcf.vcf)]), (RodBindingCollection [(RodBinding name=variant17 source=/mnt/hds/proj/cust003/analysis/exomes/145-1-2A/mosaik/GATK/145-1-2A_lanes_111222_sorted_merged_pmd_rreal_brecal_gvcf.vcf)]), (RodBindingCollection [(RodBinding name=variant18 source=/mnt/hds/proj/cust003/analysis/exomes/146-1-2A/mosaik/GATK/146-1-2A_lanes_1122_sorted_merged_pmd_rreal_brecal_gvcf.vcf)]), (RodBindingCollection [(RodBinding name=variant19 source=/mnt/hds/proj/cust003/analysis/exomes/148-1-1A/mosaik/GATK/148-1-1A_lanes_111222_sorted_merged_pmd_rreal_brecal_gvcf.vcf)]), (RodBindingCollection [(RodBinding name=variant20 source=/mnt/hds/proj/cust003/analysis/exomes/149-1-2A/mosaik/GATK/149-1-2A_lanes_1122_sorted_merged_pmd_rreal_brecal_gvcf.vcf)]), (RodBindingCollection [(RodBinding name=variant21 source=/mnt/hds/proj/cust003/analysis/exomes/150-1-2A/mosaik/GATK/150-1-2A_lanes_1122_sorted_merged_pmd_rreal_brecal_gvcf.vcf)]), (RodBindingCollection [(RodBinding name=variant22 source=/mnt/hds/proj/cust003/analysis/exomes/151-1-1A/mosaik/GATK/151-1-1A_lanes_1122_sorted_merged_pmd_rreal_brecal_gvcf.vcf)]), (RodBindingCollection [(RodBinding name=variant23 source=/mnt/hds/proj/cust003/analysis/exomes/152-1-2A/mosaik/GATK/152-1-2A_lanes_1122_sorted_merged_pmd_rreal_brecal_gvcf.vcf)]), (RodBindingCollection [(RodBinding name=variant24 source=/mnt/hds/proj/cust003/analysis/exomes/153-1-1A/mosaik/GATK/153-1-1A_lanes_0_sorted_pmd_rreal_brecal_gvcf.vcf)]), (RodBindingCollection [(RodBinding name=variant25 source=/mnt/hds/proj/cust003/analysis/exomes/153-2-1U/mosaik/GATK/153-2-1U_lanes_0_sorted_pmd_rreal_brecal_gvcf.vcf)]), (RodBindingCollection [(RodBinding name=variant26 source=/mnt/hds/proj/cust003/analysis/exomes/153-2-2U/mosaik/GATK/153-2-2U_lanes_0_sorted_pmd_rreal_brecal_gvcf.vcf)]), (RodBindingCollection [(RodBinding name=variant27 source=/mnt/hds/proj/cust003/analysis/exomes/154-1-1A/mosaik/GATK/154-1-1A_lanes_12_sorted_merged_pmd_rreal_brecal_gvcf.vcf)]), (RodBindingCollection [(RodBinding name=variant28 source=/mnt/hds/proj/cust003/analysis/exomes/27-1-1A/mosaik/GATK/27-1-1A_lanes_1122_sorted_merged_pmd_rreal_brecal_gvcf.vcf)]), (RodBindingCollection [(RodBinding name=variant29 source=/mnt/hds/proj/cust003/analysis/exomes/27-1-3A/mosaik/GATK/27-1-3A_lanes_12_sorted_merged_pmd_rreal_brecal_gvcf.vcf)]), (RodBindingCollection [(RodBinding name=variant30 source=/mnt/hds/proj/cust003/analysis/exomes/27-2-1U/mosaik/GATK/27-2-1U_lanes_111222_sorted_merged_pmd_rreal_brecal_gvcf.vcf)]), (RodBindingCollection [(RodBinding name=variant31 source=/mnt/hds/proj/cust003/analysis/exomes/27-2-2U/mosaik/GATK/27-2-2U_lanes_1122_sorted_merged_pmd_rreal_brecal_gvcf.vcf)]), (RodBindingCollection [(RodBinding name=variant32 source=/mnt/hds/proj/cust003/analysis/exomes/99-1-1A/mosaik/GATK/99-1-1A_lanes_4_sorted_pmd_rreal_brecal_gvcf.vcf)]), (RodBindingCollection [(RodBinding name=variant33 source=/mnt/hds/proj/cust003/analysis/exomes/99-2-1U/mosaik/GATK/99-2-1U_lanes_5_sorted_pmd_rreal_brecal_gvcf.vcf)]), (RodBindingCollection [(RodBinding name=variant34 source=/mnt/hds/proj/cust003/analysis/exomes/99-2-2U/mosaik/GATK/99-2-2U_lanes_4_sorted_pmd_rreal_brecal_gvcf.vcf)])] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub convertToBasePairResolution=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)
##GVCFBlock=minGQ=0(inclusive),maxGQ=5(exclusive)
##INFO=<ID=1000GAF,Number=1,Type=Float,Description="Frequency in the 1000G database.">
##INFO=<ID=1000G_MAX_AF,Number=1,Type=Float,Description="The max af for thousand genomes populations.">
##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality">
##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=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=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally">
##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=CADD,Number=1,Type=Integer,Description="The CADD relative score for this alternative.">
##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing.  Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR.">
##INFO=<ID=CLNACC,Number=.,Type=String,Description="Variant Accession and Versions">
##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=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=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|TSL|APPRIS|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|SIFT|PolyPhen|DOMAINS|HGVS_OFFSET|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|LoFtool|LoF|LoF_filter|LoF_flags|LoF_info">
##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=Compounds,Number=.,Type=String,Description="List of compound pairs for this variant.The list is splitted on ',' family id is separated with compoundswith ':'. Compounds are separated with '|'.">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype">
##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio.  Ratio between depth in samples with each called alternate allele and those without.">
##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=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=EXACAF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=EXACMAXAF,Number=A,Type=Float,Description="Estimated max allele frequency in the range (0,1) in Exac">
##INFO=<ID=EXACMAX_AF,Number=A,Type=Float,Description="Maximum Allele Frequency for variant, across populations">
##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=GERP++_RS_prediction_term,Number=A,Type=String,Description="GERP RS conservation prediction term">
##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout.">
##INFO=<ID=GeneticModels,Number=.,Type=String,Description="':'-separated list of genetic models for this variant.">
##INFO=<ID=HOB,Number=1,Type=Float,Description="Bias in the number of HOMs number (smaller is better)">
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
##INFO=<ID=ICB,Number=1,Type=Float,Description="Inbreeding Coefficient Binomial test (bigger is better)">
##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##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=LEN,Number=A,Type=Integer,Description="allele length">
##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=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles.">
##INFO=<ID=MIN,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
##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=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles">
##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
##INFO=<ID=MTAF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=ModelScore,Number=.,Type=String,Description="PHRED score for genotype models.">
##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=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'">
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position.">
##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best.">
##INFO=<ID=OLD_MULTIALLELIC,Number=1,Type=String,Description="Original chr:pos:ref:alt encoding">
##INFO=<ID=OLD_VARIANT,Number=.,Type=String,Description="Original chr:pos:ref:alt encoding">
##INFO=<ID=Obs,Number=1,Type=Integer,Description="The number of observations for the variant">
##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments">
##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments">
##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally">
##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=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations">
##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations">
##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally">
##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
##INFO=<ID=RAW_MQ,Number=1,Type=Float,Description="Raw data for RMS Mapping Quality">
##INFO=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally">
##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele">
##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele">
##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome">
##INFO=<ID=RankResult,Number=.,Type=String,Description="Splicing|Variant_call_quality_filter|Inheritance_Models|Clinical_significance|Consequence|Gene_intolerance_prediction|Conservation|allele_frequency|Deleteriousness|Protein_prediction">
##INFO=<ID=RankScore,Number=.,Type=String,Description="The rank score for this variant in this family. family_id:rank_score.">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand">
##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand">
##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
##INFO=<ID=SPIDEX,Number=1,Type=Float,Description="Z score from the spidex database.">
##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand">
##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand">
##INFO=<ID=SWEREFAC_Hemi,Number=A,Type=Integer,Description="Allele counts in hemizygous genotypes">
##INFO=<ID=SWEREFAC_Het,Number=A,Type=Integer,Description="Allele counts in heterozygous genotypes">
##INFO=<ID=SWEREFAC_Hom,Number=A,Type=Integer,Description="Allele counts in homozygous genotypes">
##INFO=<ID=SWEREFAF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=SnpSift_AF,Number=.,Type=String,Description="Estimated max allele frequency in the range (0,1)">
##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)">
##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">
##INFO=<ID=dbNSFP_GERP___NR,Number=A,Type=Float,Description="Field 'GERP++_NR' from dbNSFP">
##INFO=<ID=dbNSFP_GERP___RS,Number=A,Type=Float,Description="Field 'GERP++_RS' from dbNSFP">
##INFO=<ID=dbNSFP_phastCons100way_vertebrate,Number=A,Type=Float,Description="Field 'phastCons100way_vertebrate' from dbNSFP">
##INFO=<ID=dbNSFP_phastCons46way_primate,Number=A,Type=Float,Description="Field 'phastCons46way_primate' from dbNSFP">
##INFO=<ID=dbNSFP_phyloP100way_vertebrate,Number=A,Type=Float,Description="Field 'phyloP100way_vertebrate' from dbNSFP">
##INFO=<ID=dbNSFP_phyloP46way_primate,Number=A,Type=Float,Description="Field 'phyloP46way_primate' from dbNSFP">
##INFO=<ID=most_severe_consequence,Number=.,Type=String,Description="Most severe genomic consequence.">
##INFO=<ID=phastCons100way_vertebrate_prediction_term,Number=A,Type=String,Description="PhastCons conservation prediction term">
##INFO=<ID=phyloP100way_vertebrate_prediction_term,Number=A,Type=String,Description="PhyloP conservation prediction term">
##INFO=<ID=set,Number=1,Type=String,Description="Source VCF for the merged record in CombineVariants">
##INFO=<ID=technology.ILLUMINA,Number=A,Type=Float,Description="Fraction of observations supporting the alternate observed in reads from ILLUMINA">
##INFO=<ID=AZLENGTH,Number=1,Type=String,Description="Autozygous region length">
##INFO=<ID=AZQUAL,Number=1,Type=String,Description="Autozygous positon call quality">
##LoF=Loss-of-function annotation (HC = High Confidence; LC = Low Confidence)
##LoF_filter=Reason for LoF not being HC
##LoF_flags=Possible warning flags for LoF
##LoF_info=Info used for LoF annotation
##LoFtool=LoFtool score for gene
##SnpEffCmd="SnpEff  GRCh37.75 /scratch/717414/internal_id_sorted_md_brecal_gvcf_vrecal_comb_vt_vep_parsed_BOTH_1.selected.vcf "
##SnpEffVersion="4.2 (build 2015-12-05), by Pablo Cingolani"
##SnpSiftCmd="SnpSift dbnsfp -f GERP++_RS,GERP++_NR,phyloP46way_primate,phyloP100way_vertebrate,phastCons46way_primate,phastCons100way_vertebrate /scratch/717414/internal_id_sorted_md_brecal_gvcf_vrecal_comb_vt_vep_parsed_BOTH_1.selected.vcf.20"
##SnpSiftVersion="SnpSift 4.2 (build 2015-12-05), by Pablo Cingolani"
##Software=<ID=genmod,Version=3.5.9,Date="2016-12-08 18:23",CommandLineOptions="processes=4 keyword=Annotation family_file=<open file '/mnt/hds/proj/bioinfo/develop/henrikS/internal_id/analysis/internal_id/internal_id.fam', mode 'r' at 0x7f3470cd9c90> family_type=ped reduced_penetrance=<open file '/mnt/hds/proj/bioinfo/develop/references_4.0/cust003-CMMS-red-pen.txt.csv', mode 'r' at 0x7f3470cd9c00> outfile=<unopened file '/dev/stdout' w> temp_dir=/scratch/717414 variant_file=/scratch/717414/internal_id_sorted_md_brecal_gvcf_vrecal_comb_vt_vep_parsed_snpeff_BOTH_1.selected.vcf whole_gene=True logger=<logging.Logger object at 0x7f34709fbc50> vep=True">
##VEP=v85 cache=/mnt/hds/proj/bioinfo/components/maintainance/miniconda/envs/mip4.0/ensembl-tools-release-85/cache/homo_sapiens/85_GRCh37 db=. assembly=GRCh37.p13 genebuild=2011-04 COSMIC=71 ClinVar=201507 regbuild=13 HGMD-PUBLIC=20152 ESP=20141103 gencode=GENCODE 19 sift=sift5.2.2 dbSNP=144 polyphen=2.2.2
##bcftools_callCommand=call --format-fields GQ -v -m --samples-file /mnt/hds/proj/bioinfo/develop/henrikS/internal_id/analysis/internal_id/bwa/samtools/internal_id.fam --constrain trio
##bcftools_callVersion=1.3.1+htslib-1.3.1
##bcftools_filterCommand=filter -sLowQual -g3 -G10 -e '%QUAL<10 || (RPB<0.1 && %QUAL<15) || (AC<2 && %QUAL<15) || %MAX(DV)<=3 || %MAX(DV)/%MAX(DP)<=0.25'
##bcftools_filterVersion=1.3.1+htslib-1.3.1
##bcftools_normCommand=norm --multiallelics -both -f /mnt/hds/proj/bioinfo/develop/references_4.0/Homo_sapiens.GRCh37.d5.fasta -o /scratch/717408/internal_id_sorted_md_brecal_gvcf_vrecal_BOTH_normalized.vcf /scratch/717408/internal_id_sorted_md_brecal_gvcf_vrecal_BOTH.vcf
##bcftools_normVersion=1.3.1+htslib-1.3.1
##commandline="freebayes --standard-filters --genotype-qualities --fasta-reference /mnt/hds/proj/bioinfo/develop/references_4.0/Homo_sapiens.GRCh37.d5.fasta /scratch/717379/ADM1059A1_lanes_1_sorted_md_brecal_1.bam /scratch/717379/ADM1059A2_lanes_1_sorted_md_brecal_1.bam /scratch/717379/ADM1059A3_lanes_1_sorted_md_brecal_1.bam"
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##fileDate=20161208
##phasing=none
##reference=file:///mnt/hds/proj/bioinfo/develop/references_4.0/Homo_sapiens.GRCh37.d5.fasta
##samtoolsCommand=samtools mpileup -g -C 50 -p -t DV,AD -f /mnt/hds/proj/bioinfo/develop/references_4.0/Homo_sapiens.GRCh37.d5.fasta /scratch/717378/ADM1059A1_lanes_1_sorted_md_brecal_1.bam /scratch/717378/ADM1059A2_lanes_1_sorted_md_brecal_1.bam /scratch/717378/ADM1059A3_lanes_1_sorted_md_brecal_1.bam
##samtoolsVersion=1.3.1+htslib-1.3.1
##source=CalculateGenotypePosteriors
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	ADM1059A1	ADM1059A2	ADM1059A3
1	156146640	rs41265017	G	A	12083.90	PASS	1000GAF=0.0217652;1000G_MAX_AF=0.0636;AB=0.478873;ABP=3.28556;AC=2;AF=0.333;AN=6;ANN=A|missense_variant|MODERATE|SEMA4A|ENSG00000196189|transcript|ENST00000355014|protein_coding|15/15|c.2138G>A|p.Arg713Gln|2242/3137|2138/2286|713/761||,A|missense_variant|MODERATE|SEMA4A|ENSG00000196189|transcript|ENST00000368285|protein_coding|15/15|c.2138G>A|p.Arg713Gln|2405/3300|2138/2286|713/761||,A|missense_variant|MODERATE|SEMA4A|ENSG00000196189|transcript|ENST00000368284|protein_coding|13/13|c.1742G>A|p.Arg581Gln|2087/2981|1742/1890|581/629||,A|missense_variant|MODERATE|SEMA4A|ENSG00000196189|transcript|ENST00000368286|protein_coding|14/14|c.1742G>A|p.Arg581Gln|2236/3130|1742/1890|581/629||,A|missense_variant|MODERATE|SEMA4A|ENSG00000196189|transcript|ENST00000368282|protein_coding|14/14|c.2138G>A|p.Arg713Gln|2346/3249|2138/2286|713/761||,A|sequence_feature|LOW|SEMA4A|ENSG00000196189|topological_domain:Cytoplasmic|ENST00000355014|protein_coding|15/15|c.2138G>A||||||,A|sequence_feature|LOW|SEMA4A|ENSG00000196189|topological_domain:Cytoplasmic|ENST00000368284|protein_coding|13/13|c.1742G>A||||||,A|downstream_gene_variant|MODIFIER|SEMA4A|ENSG00000196189|transcript|ENST00000487358|processed_transcript||n.*1617G>A|||||1617|,A|downstream_gene_variant|MODIFIER|SEMA4A|ENSG00000196189|transcript|ENST00000462892|retained_intron||n.*1202G>A|||||1202|,A|downstream_gene_variant|MODIFIER|SEMA4A|ENSG00000196189|transcript|ENST00000484155|processed_transcript||n.*193G>A|||||193|;AO=34;BQB=0.403626;BaseQRankSum=2.32;CADD=21.0;CIGAR=1X;CLNACC=RCV000003528.4|RCV000174949.1;CLNREVSTAT=no_criteria|mult;CLNSIG=5|2;CSQ=A|missense_variant|MODERATE|SEMA4A|ENSG00000196189|Transcript|ENST00000355014|protein_coding|15/15||ENST00000355014.2:c.2138G>A|ENSP00000347117.2:p.Arg713Gln|2242|2138|713|R/Q|cGg/cAg|||1||HGNC|10729||||CCDS1132.1|ENSP00000347117|Q9H3S1|Q9HA40&Q5TCJ7&Q5TCJ5&Q5TCI6&B4DKS5|UPI000007217A|tolerated|benign|hmmpanther:PTHR11036:SF15&hmmpanther:PTHR11036||||||0.895||||,A|missense_variant|MODERATE|SEMA4A|ENSG00000196189|Transcript|ENST00000368282|protein_coding|14/14||ENST00000368282.1:c.2138G>A|ENSP00000357265.1:p.Arg713Gln|2346|2138|713|R/Q|cGg/cAg|||1||HGNC|10729||||CCDS1132.1|ENSP00000357265|Q9H3S1|Q9HA40&Q5TCJ7&Q5TCJ5&Q5TCI6&B4DKS5|UPI000007217A|tolerated|benign|hmmpanther:PTHR11036&hmmpanther:PTHR11036:SF15||||||0.895||||,A|missense_variant|MODERATE|SEMA4A|ENSG00000196189|Transcript|ENST00000368284|protein_coding|13/13||ENST00000368284.1:c.1742G>A|ENSP00000357267.1:p.Arg581Gln|2087|1742|581|R/Q|cGg/cAg|||1||HGNC|10729||||CCDS53378.1|ENSP00000357267|Q9H3S1|Q9HA40|UPI000046FD07|tolerated|benign|hmmpanther:PTHR11036&hmmpanther:PTHR11036:SF15||||||0.895||||,A|missense_variant|MODERATE|SEMA4A|ENSG00000196189|Transcript|ENST00000368285|protein_coding|15/15||ENST00000368285.3:c.2138G>A|ENSP00000357268.3:p.Arg713Gln|2405|2138|713|R/Q|cGg/cAg|||1||HGNC|10729|YES|||CCDS1132.1|ENSP00000357268|Q9H3S1|Q9HA40&Q5TCJ7&Q5TCJ5&Q5TCI6&B4DKS5|UPI000007217A|tolerated|benign|hmmpanther:PTHR11036&hmmpanther:PTHR11036:SF15||||||0.895||||,A|missense_variant|MODERATE|SEMA4A|ENSG00000196189|Transcript|ENST00000368286|protein_coding|14/14||ENST00000368286.2:c.1742G>A|ENSP00000357269.2:p.Arg581Gln|2236|1742|581|R/Q|cGg/cAg|||1||HGNC|10729||||CCDS53378.1|ENSP00000357269|Q9H3S1|Q9HA40|UPI000046FD07|tolerated|benign|hmmpanther:PTHR11036&hmmpanther:PTHR11036:SF15||||||0.895||||,A|downstream_gene_variant|MODIFIER|SEMA4A|ENSG00000196189|Transcript|ENST00000462892|retained_intron|||||||||||1202|1||HGNC|10729|||||||||||||||||0.895||||,A|downstream_gene_variant|MODIFIER|SEMA4A|ENSG00000196189|Transcript|ENST00000484155|processed_transcript|||||||||||193|1||HGNC|10729|||||||||||||||||0.895||||,A|downstream_gene_variant|MODIFIER|SEMA4A|ENSG00000196189|Transcript|ENST00000487358|processed_transcript|||||||||||1617|1||HGNC|10729|||||||||||||||||0.895||||:ENST00000355014:missense_variant:ENST00000368282:missense_variant:ENST00000368284:missense_variant:ENST00000368285:missense_variant:ENST00000368286:missense_variant:ENST00000462892:downstream_gene_variant:ENST00000484155:downstream_gene_variant:ENST00000487358:downstream_gene_variant;ClippingRankSum=0;Compounds=clinvar:1_156126553_G_T>-2|1_156131050_A_T>-12;DB;DP=321;DP4=41,32,16,16;DPB=107;DPRA=0.986111;EPP=7.09778;EPPR=11.607;EXACAF=0.035;EXACMAX_AF=0.0517621145374449;ExcessHet=3.3908;FS=2.452;GTI=0;GeneticModels=clinvar:AR_comp;HOB=0.222222;ICB=0.8;InbreedingCoeff=-0.0588;LEN=1;MEANALT=1;MQ0=0;MQ0F=0;MQB=1.51321e-09;MQM=60;MQMR=60;MQRankSum=0;MQSB=0.995953;ModelScore=clinvar:94;NS=3;NUMALT=1;ODDS=32.3506;Obs=43;PAIRED=1;PAIREDR=1;PAO=0;PG=0,13,33;POSITIVE_TRAIN_SITE;PQA=0;PQR=0;PRO=0;QA=1230;QD=16.46;QR=2540;RO=73;RPB=0.630365;RPL=17;RPP=3.0103;RPPR=3.04005;RPR=17;RUN=1;RankResult=0|3|1|2|5|0|2|-12|3|0;RankScore=clinvar:15;ReadPosRankSum=-0.232;SAF=18;SAP=3.26577;SAR=16;SGB=0.229082;SOR=0.539;SRF=41;SRP=5.41974;SRR=32;SWEREFAC_Hemi=0;SWEREFAC_Het=44;SWEREFAC_Hom=4;SWEREFAF=0.024;TYPE=snp;VDB=0.333514;VQSLOD=0.265;culprit=MQ;dbNSFP_GERP___NR=5.18;dbNSFP_GERP___RS=4.16;dbNSFP_phastCons100way_vertebrate=1.000000;dbNSFP_phastCons46way_primate=0.481000;dbNSFP_phyloP100way_vertebrate=2.218000;dbNSFP_phyloP46way_primate=0.306000;most_severe_consequence=10729:A|missense_variant;phastCons100way_vertebrate_prediction_term=Conserved;phyloP100way_vertebrate_prediction_term=NotConserved;set=gatk-filterInsamtools-freebayes;technology.ILLUMINA=1	GT:AD:DP:GQ:JL:JP:PL:PP	0/1:18,16:34:99:105:105:514,0,609:561,0,628	0/1:18,14:32:99:105:105:519,0,629:506,0,708	0/0:35,0:35:99:105:105:0,105,1334:0,118,1367
1	210267893	rs2307890;rs144713062	TGAA	T	37405.70	PASS	1000GAF=0.0796725;1000G_MAX_AF=0.1421;AB=0.434211;ABP=5.8675;AC=2;AF=0.333;AN=6;ANN=T|disruptive_inframe_deletion|MODERATE|SYT14|ENSG00000143469|transcript|ENST00000422431|protein_coding|6/10|c.810_812delAGA|p.Glu270del|868/5162|810/1860|270/619||INFO_REALIGN_3_PRIME,T|disruptive_inframe_deletion|MODERATE|SYT14|ENSG00000143469|transcript|ENST00000399639|protein_coding|5/10|c.675_677delAGA|p.Glu225del|747/5043|675/1377|225/458||INFO_REALIGN_3_PRIME,T|disruptive_inframe_deletion|MODERATE|SYT14|ENSG00000143469|transcript|ENST00000534859|protein_coding|5/9|c.675_677delAGA|p.Glu225del|747/5062|675/1746|225/581||INFO_REALIGN_3_PRIME,T|disruptive_inframe_deletion|MODERATE|SYT14|ENSG00000143469|transcript|ENST00000537238|protein_coding|6/9|c.561_563delAGA|p.Glu187del|952/5189|561/1554|187/517||INFO_REALIGN_3_PRIME,T|disruptive_inframe_deletion|MODERATE|SYT14|ENSG00000143469|transcript|ENST00000367019|protein_coding|5/9|c.675_677delAGA|p.Glu225del|709/2940|675/1725|225/574||INFO_REALIGN_3_PRIME,T|disruptive_inframe_deletion|MODERATE|SYT14|ENSG00000143469|transcript|ENST00000472886|protein_coding|5/8|c.675_677delAGA|p.Glu225del|689/2966|675/1668|225/555||INFO_REALIGN_3_PRIME,T|disruptive_inframe_deletion|MODERATE|SYT14|ENSG00000143469|transcript|ENST00000367015|protein_coding|5/8|c.561_563delAGA|p.Glu187del|867/5109|561/1554|187/517||INFO_REALIGN_3_PRIME,T|sequence_feature|LOW|SYT14|ENSG00000143469|topological_domain:Cytoplasmic|ENST00000472886|protein_coding|7/8|c.670_672delGAA||||||,T|non_coding_exon_variant|MODIFIER|SYT14|ENSG00000143469|transcript|ENST00000271745|processed_transcript|5/8|n.867_869delAGA||||||INFO_REALIGN_3_PRIME,T|non_coding_exon_variant|MODIFIER|SYT14|ENSG00000143469|transcript|ENST00000469604|processed_transcript|2/6|n.442_444delAGA||||||INFO_REALIGN_3_PRIME;AO=33;BaseQRankSum=0.132;CADD=19.60;CIGAR=1M3D4M;CLNACC=RCV000195198.2,RCV000195198.2;CLNREVSTAT=single,single;CLNSIG=4,0;CSQ=-|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|SYT14|ENSG00000143469|Transcript|ENST00000271745|processed_transcript|5/8||ENST00000271745.7:n.867_869delAGA||862-864|||||||1||HGNC|23143||||||||||||5|||||0.294||||,-|inframe_deletion|MODERATE|SYT14|ENSG00000143469|Transcript|ENST00000367015|protein_coding|5/8||ENST00000367015.1:c.561_563delAGA|ENSP00000355982.1:p.Glu187del|862-864|556-558|186|E/-|GAA/-|||1||HGNC|23143||||CCDS58058.1|ENSP00000355982|Q8NB59||UPI000022841A|||hmmpanther:PTHR10024:SF209&hmmpanther:PTHR10024|5|||||0.294||||,-|inframe_deletion|MODERATE|SYT14|ENSG00000143469|Transcript|ENST00000367019|protein_coding|5/9||ENST00000367019.1:c.675_677delAGA|ENSP00000355986.1:p.Glu225del|704-706|670-672|224|E/-|GAA/-|||1||HGNC|23143||||CCDS53470.1|ENSP00000355986|Q8NB59||UPI000046FCC9|||hmmpanther:PTHR10024&hmmpanther:PTHR10024:SF209|5|||||0.294||||,-|inframe_deletion|MODERATE|SYT14|ENSG00000143469|Transcript|ENST00000399639|protein_coding|5/10||ENST00000399639.2:c.675_677delAGA|ENSP00000445837.1:p.Glu225del|742-744|670-672|224|E/-|GAA/-|||1||HGNC|23143|||||ENSP00000445837||F5H1A2|UPI0002065159|||hmmpanther:PTHR10024&hmmpanther:PTHR10024:SF209|5|||||0.294||||,-|inframe_deletion|MODERATE|SYT14|ENSG00000143469|Transcript|ENST00000422431|protein_coding|6/10||ENST00000422431.1:c.810_812delAGA|ENSP00000389039.1:p.Glu270del|863-865|805-807|269|E/-|GAA/-|||1||HGNC|23143|YES|||CCDS53469.1|ENSP00000389039|Q8NB59|A1L3Y1|UPI0001639EBD|||hmmpanther:PTHR10024&hmmpanther:PTHR10024:SF209|5|||||0.294||||,-|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|SYT14|ENSG00000143469|Transcript|ENST00000469604|processed_transcript|2/6||ENST00000469604.1:n.442_444delAGA||437-439|||||||1||HGNC|23143||||||||||||5|||||0.294||||,-|inframe_deletion|MODERATE|SYT14|ENSG00000143469|Transcript|ENST00000472886|protein_coding|5/8||ENST00000472886.1:c.675_677delAGA|ENSP00000418901.1:p.Glu225del|684-686|670-672|224|E/-|GAA/-|||1||HGNC|23143||||CCDS31014.1|ENSP00000418901|Q8NB59||UPI0000205DDE|||hmmpanther:PTHR10024&hmmpanther:PTHR10024:SF209|5|||||0.294||||,-|inframe_deletion|MODERATE|SYT14|ENSG00000143469|Transcript|ENST00000534859|protein_coding|5/9||ENST00000534859.1:c.675_677delAGA|ENSP00000442891.1:p.Glu225del|742-744|670-672|224|E/-|GAA/-|||1||HGNC|23143|||||ENSP00000442891|Q8NB59||UPI00004DE6A1|||hmmpanther:PTHR10024&hmmpanther:PTHR10024:SF209|5|||||0.294||||,-|inframe_deletion|MODERATE|SYT14|ENSG00000143469|Transcript|ENST00000537238|protein_coding|6/9||ENST00000537238.1:c.561_563delAGA|ENSP00000437423.1:p.Glu187del|947-949|556-558|186|E/-|GAA/-|||1||HGNC|23143||||CCDS58058.1|ENSP00000437423|Q8NB59||UPI000022841A|||hmmpanther:PTHR10024&hmmpanther:PTHR10024:SF209|5|||||0.294||||:ENST00000271745:non_coding_transcript_exon_variant&non_coding_transcript_variant:ENST00000367015:inframe_deletion:ENST00000367019:inframe_deletion:ENST00000399639:inframe_deletion:ENST00000422431:inframe_deletion:ENST00000469604:non_coding_transcript_exon_variant&non_coding_transcript_variant:ENST00000472886:inframe_deletion:ENST00000534859:inframe_deletion:ENST00000537238:inframe_deletion;ClippingRankSum=0;DB;DP=368;DP4=47,37,18,22;DPB=108.5;DPRA=0.95;EPP=3.0761;EPPR=3.11623;EXACAF=0.117;EXACMAX_AF=0.212856276531231;ExcessHet=2.0591;FS=0;GTI=0;HOB=0.222222;ICB=0.8;IDV=25;IMF=0.510204;INDEL;InbreedingCoeff=0.0343;LEN=3;MEANALT=1.5;MQ0=0;MQ0F=0;MQM=60;MQMR=60;MQRankSum=0;MQSB=0.911585;NEGATIVE_TRAIN_SITE;NS=3;NUMALT=1;ODDS=40.8904;Obs=114;PAIRED=1;PAIREDR=1;PAO=4;PG=0,0,0;POSITIVE_TRAIN_SITE;PQA=110;PQR=177;PRO=6;QA=1110;QD=23.28;QR=2931;RO=82;RPL=16;RPP=3.0761;RPPR=13.6028;RPR=17;RUN=1;RankResult=0|3|-12|1|5|0|0|-12|2|0;RankScore=clinvar:3;ReadPosRankSum=1.18;SAF=14;SAP=4.65535;SAR=19;SGB=1.01798;SOR=0.645;SRF=45;SRP=4.70511;SRR=37;SWEREFAC_Hemi=0;SWEREFAC_Het=231;SWEREFAC_Hom=40;SWEREFAF=0.136;TYPE=del;VDB=0.203753;VQSLOD=-0.4969;culprit=FS;most_severe_consequence=23143:-|inframe_deletion;set=filterIngatk-samtools-freebayes;technology.ILLUMINA=1	GT:AD:DP:GQ:JL:JP:PL:PP	0/1:24,14:38:99:102:102:516,0,1122:516,0,1182	0/0:38,0:38:99:102:102:0,103,1354:0,103,1354	0/1:19,23:42:99:102:102:907,0,870:907,0,930
