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  1. ##fileformat=VCFv4.1
  2. ##FILTER=<ID=PASS,Description="All filters passed">
  3. ##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
  4. ##FILTER=<ID=LowQual,Description="Low quality">
  5. ##FILTER=<ID=VQSRTrancheINDEL99.00to99.90,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -3.3779 <= x < -0.2719">
  6. ##FILTER=<ID=VQSRTrancheINDEL99.90to100.00+,Description="Truth sensitivity tranche level for INDEL model at VQS Lod < -200.3104">
  7. ##FILTER=<ID=VQSRTrancheINDEL99.90to100.00,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -200.3104 <= x < -3.3779">
  8. ##FILTER=<ID=VQSRTrancheSNP99.00to99.90,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -3.8305 <= x < 0.5939">
  9. ##FILTER=<ID=VQSRTrancheSNP99.90to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -172.2792">
  10. ##FILTER=<ID=VQSRTrancheSNP99.90to100.00,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -172.2792 <= x < -3.8305">
  11. ##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
  12. ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
  13. ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
  14. ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
  15. ##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
  16. ##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
  17. ##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">
  18. ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
  19. ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
  20. ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
  21. ##GATKCommandLine.ApplyRecalibration.2=<ID=ApplyRecalibration,Version=3.4-46-gbc02625,Date="Wed Mar 30 00:13:30 CEST 2016",Epoch=1459289610308,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=/data/annos/grch37.p13/grch37.p13.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 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=ALL 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=12 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 input=[(RodBinding name=input source=sy244.recalibrated_snps_raw_indels.vcf.gz)] recal_file=(RodBinding name=recal_file source=sy244.recalibrate_INDEL.recal) tranches_file=sy244.recalibrate_INDEL.tranches out=/archive/sample_data/sy244/sy244.recalibrated_variants.vcf.gz 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">
  22. ##GATKCommandLine.ApplyRecalibration=<ID=ApplyRecalibration,Version=3.4-46-gbc02625,Date="Wed Mar 30 00:11:10 CEST 2016",Epoch=1459289470693,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=/data/annos/grch37.p13/grch37.p13.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 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=ALL 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=12 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 input=[(RodBinding name=input source=sy244_joint.vcf.gz)] recal_file=(RodBinding name=recal_file source=sy244.recalibrate_SNP.recal) tranches_file=sy244.recalibrate_SNP.tranches out=/archive/sample_data/sy244/sy244.recalibrated_snps_raw_indels.vcf.gz ts_filter_level=99.0 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">
  23. ##GATKCommandLine.GenotypeGVCFs=<ID=GenotypeGVCFs,Version=3.4-46-gbc02625,Date="Tue Mar 29 23:52:05 CEST 2016",Epoch=1459288325575,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=/data/annos/grch37.p13/grch37.p13.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 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=ALL 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=12 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=sy244pa.raw_variants.g.vcf.gz)])] out=/archive/sample_data/sy244/sy244_joint.vcf.gz 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=12 input_prior=[] sample_ploidy=2 annotation=[InbreedingCoeff, FisherStrand, QualByDepth, ChromosomeCounts, StrandOddsRatio] dbsnp=(RodBinding name= source=UNBOUND) filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
  24. ##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.4-46-gbc02625,Date="Tue Mar 29 15:43:00 CEST 2016",Epoch=1459258980210,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[fastq/sy244pa/sy244pa.recal.bam] 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=/data/annos/grch37.p13/grch37.p13.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 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=ALL 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=12 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=LINEAR variant_index_parameter=128000 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=[ClippingRankSumTest, DepthPerSampleHC, StrandBiasBySample] excludeAnnotation=[ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] 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">
  25. ##GVCFBlock0-1=minGQ=0(inclusive),maxGQ=1(exclusive)
  26. ##GVCFBlock1-2=minGQ=1(inclusive),maxGQ=2(exclusive)
  27. ##GVCFBlock10-11=minGQ=10(inclusive),maxGQ=11(exclusive)
  28. ##GVCFBlock11-12=minGQ=11(inclusive),maxGQ=12(exclusive)
  29. ##GVCFBlock12-13=minGQ=12(inclusive),maxGQ=13(exclusive)
  30. ##GVCFBlock13-14=minGQ=13(inclusive),maxGQ=14(exclusive)
  31. ##GVCFBlock14-15=minGQ=14(inclusive),maxGQ=15(exclusive)
  32. ##GVCFBlock15-16=minGQ=15(inclusive),maxGQ=16(exclusive)
  33. ##GVCFBlock16-17=minGQ=16(inclusive),maxGQ=17(exclusive)
  34. ##GVCFBlock17-18=minGQ=17(inclusive),maxGQ=18(exclusive)
  35. ##GVCFBlock18-19=minGQ=18(inclusive),maxGQ=19(exclusive)
  36. ##GVCFBlock19-20=minGQ=19(inclusive),maxGQ=20(exclusive)
  37. ##GVCFBlock2-3=minGQ=2(inclusive),maxGQ=3(exclusive)
  38. ##GVCFBlock20-21=minGQ=20(inclusive),maxGQ=21(exclusive)
  39. ##GVCFBlock21-22=minGQ=21(inclusive),maxGQ=22(exclusive)
  40. ##GVCFBlock22-23=minGQ=22(inclusive),maxGQ=23(exclusive)
  41. ##GVCFBlock23-24=minGQ=23(inclusive),maxGQ=24(exclusive)
  42. ##GVCFBlock24-25=minGQ=24(inclusive),maxGQ=25(exclusive)
  43. ##GVCFBlock25-26=minGQ=25(inclusive),maxGQ=26(exclusive)
  44. ##GVCFBlock26-27=minGQ=26(inclusive),maxGQ=27(exclusive)
  45. ##GVCFBlock27-28=minGQ=27(inclusive),maxGQ=28(exclusive)
  46. ##GVCFBlock28-29=minGQ=28(inclusive),maxGQ=29(exclusive)
  47. ##GVCFBlock29-30=minGQ=29(inclusive),maxGQ=30(exclusive)
  48. ##GVCFBlock3-4=minGQ=3(inclusive),maxGQ=4(exclusive)
  49. ##GVCFBlock30-31=minGQ=30(inclusive),maxGQ=31(exclusive)
  50. ##GVCFBlock31-32=minGQ=31(inclusive),maxGQ=32(exclusive)
  51. ##GVCFBlock32-33=minGQ=32(inclusive),maxGQ=33(exclusive)
  52. ##GVCFBlock33-34=minGQ=33(inclusive),maxGQ=34(exclusive)
  53. ##GVCFBlock34-35=minGQ=34(inclusive),maxGQ=35(exclusive)
  54. ##GVCFBlock35-36=minGQ=35(inclusive),maxGQ=36(exclusive)
  55. ##GVCFBlock36-37=minGQ=36(inclusive),maxGQ=37(exclusive)
  56. ##GVCFBlock37-38=minGQ=37(inclusive),maxGQ=38(exclusive)
  57. ##GVCFBlock38-39=minGQ=38(inclusive),maxGQ=39(exclusive)
  58. ##GVCFBlock39-40=minGQ=39(inclusive),maxGQ=40(exclusive)
  59. ##GVCFBlock4-5=minGQ=4(inclusive),maxGQ=5(exclusive)
  60. ##GVCFBlock40-41=minGQ=40(inclusive),maxGQ=41(exclusive)
  61. ##GVCFBlock41-42=minGQ=41(inclusive),maxGQ=42(exclusive)
  62. ##GVCFBlock42-43=minGQ=42(inclusive),maxGQ=43(exclusive)
  63. ##GVCFBlock43-44=minGQ=43(inclusive),maxGQ=44(exclusive)
  64. ##GVCFBlock44-45=minGQ=44(inclusive),maxGQ=45(exclusive)
  65. ##GVCFBlock45-46=minGQ=45(inclusive),maxGQ=46(exclusive)
  66. ##GVCFBlock46-47=minGQ=46(inclusive),maxGQ=47(exclusive)
  67. ##GVCFBlock47-48=minGQ=47(inclusive),maxGQ=48(exclusive)
  68. ##GVCFBlock48-49=minGQ=48(inclusive),maxGQ=49(exclusive)
  69. ##GVCFBlock49-50=minGQ=49(inclusive),maxGQ=50(exclusive)
  70. ##GVCFBlock5-6=minGQ=5(inclusive),maxGQ=6(exclusive)
  71. ##GVCFBlock50-51=minGQ=50(inclusive),maxGQ=51(exclusive)
  72. ##GVCFBlock51-52=minGQ=51(inclusive),maxGQ=52(exclusive)
  73. ##GVCFBlock52-53=minGQ=52(inclusive),maxGQ=53(exclusive)
  74. ##GVCFBlock53-54=minGQ=53(inclusive),maxGQ=54(exclusive)
  75. ##GVCFBlock54-55=minGQ=54(inclusive),maxGQ=55(exclusive)
  76. ##GVCFBlock55-56=minGQ=55(inclusive),maxGQ=56(exclusive)
  77. ##GVCFBlock56-57=minGQ=56(inclusive),maxGQ=57(exclusive)
  78. ##GVCFBlock57-58=minGQ=57(inclusive),maxGQ=58(exclusive)
  79. ##GVCFBlock58-59=minGQ=58(inclusive),maxGQ=59(exclusive)
  80. ##GVCFBlock59-60=minGQ=59(inclusive),maxGQ=60(exclusive)
  81. ##GVCFBlock6-7=minGQ=6(inclusive),maxGQ=7(exclusive)
  82. ##GVCFBlock60-70=minGQ=60(inclusive),maxGQ=70(exclusive)
  83. ##GVCFBlock7-8=minGQ=7(inclusive),maxGQ=8(exclusive)
  84. ##GVCFBlock70-80=minGQ=70(inclusive),maxGQ=80(exclusive)
  85. ##GVCFBlock8-9=minGQ=8(inclusive),maxGQ=9(exclusive)
  86. ##GVCFBlock80-90=minGQ=80(inclusive),maxGQ=90(exclusive)
  87. ##GVCFBlock9-10=minGQ=9(inclusive),maxGQ=10(exclusive)
  88. ##GVCFBlock90-99=minGQ=90(inclusive),maxGQ=99(exclusive)
  89. ##GVCFBlock99-2147483647=minGQ=99(inclusive),maxGQ=2147483647(exclusive)
  90. ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
  91. ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
  92. ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
  93. ##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
  94. ##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
  95. ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
  96. ##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
  97. ##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
  98. ##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
  99. ##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
  100. ##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">
  101. ##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">
  102. ##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">
  103. ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
  104. ##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
  105. ##INFO=<ID=NEGATIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the negative training set of bad variants">
  106. ##INFO=<ID=POSITIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the positive training set of good variants">
  107. ##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
  108. ##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
  109. ##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
  110. ##INFO=<ID=VQSLOD,Number=1,Type=Float,Description="Log odds of being a true variant versus being false under the trained gaussian mixture model">
  111. ##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">
  112. ##contig=<ID=chr1,length=249250621>
  113. ##contig=<ID=chr2,length=243199373>
  114. ##contig=<ID=chr3,length=198022430>
  115. ##contig=<ID=chr4,length=191154276>
  116. ##contig=<ID=chr5,length=180915260>
  117. ##contig=<ID=chr6,length=171115067>
  118. ##contig=<ID=chr7,length=159138663>
  119. ##contig=<ID=chr8,length=146364022>
  120. ##contig=<ID=chr9,length=141213431>
  121. ##contig=<ID=chr10,length=135534747>
  122. ##contig=<ID=chr11,length=135006516>
  123. ##contig=<ID=chr12,length=133851895>
  124. ##contig=<ID=chr13,length=115169878>
  125. ##contig=<ID=chr14,length=107349540>
  126. ##contig=<ID=chr15,length=102531392>
  127. ##contig=<ID=chr16,length=90354753>
  128. ##contig=<ID=chr17,length=81195210>
  129. ##contig=<ID=chr18,length=78077248>
  130. ##contig=<ID=chr19,length=59128983>
  131. ##contig=<ID=chr20,length=63025520>
  132. ##contig=<ID=chr21,length=48129895>
  133. ##contig=<ID=chr22,length=51304566>
  134. ##contig=<ID=chrX,length=155270560>
  135. ##contig=<ID=chrY,length=59373566>
  136. ##contig=<ID=chrM,length=16569>
  137. ##contig=<ID=chr1_gl000191,length=106433>
  138. ##contig=<ID=chr1_gl000192,length=547496>
  139. ##contig=<ID=chr4_gl000193,length=189789>
  140. ##contig=<ID=chr4_gl000194,length=191469>
  141. ##contig=<ID=chr7_gl000195,length=182896>
  142. ##contig=<ID=chr8_gl000196,length=38914>
  143. ##contig=<ID=chr8_gl000197,length=37175>
  144. ##contig=<ID=chr9_gl000198,length=90085>
  145. ##contig=<ID=chr9_gl000199,length=169874>
  146. ##contig=<ID=chr9_gl000200,length=187035>
  147. ##contig=<ID=chr9_gl000201,length=36148>
  148. ##contig=<ID=chr11_gl000202,length=40103>
  149. ##contig=<ID=chr17_gl000203,length=37498>
  150. ##contig=<ID=chr17_gl000204,length=81310>
  151. ##contig=<ID=chr17_gl000205,length=174588>
  152. ##contig=<ID=chr17_gl000206,length=41001>
  153. ##contig=<ID=chr18_gl000207,length=4262>
  154. ##contig=<ID=chr19_gl000208,length=92689>
  155. ##contig=<ID=chr19_gl000209,length=159169>
  156. ##contig=<ID=chr21_gl000210,length=27682>
  157. ##contig=<ID=chrUn_gl000211,length=166566>
  158. ##contig=<ID=chrUn_gl000212,length=186858>
  159. ##contig=<ID=chrUn_gl000213,length=164239>
  160. ##contig=<ID=chrUn_gl000214,length=137718>
  161. ##contig=<ID=chrUn_gl000215,length=172545>
  162. ##contig=<ID=chrUn_gl000216,length=172294>
  163. ##contig=<ID=chrUn_gl000217,length=172149>
  164. ##contig=<ID=chrUn_gl000218,length=161147>
  165. ##contig=<ID=chrUn_gl000219,length=179198>
  166. ##contig=<ID=chrUn_gl000220,length=161802>
  167. ##contig=<ID=chrUn_gl000221,length=155397>
  168. ##contig=<ID=chrUn_gl000222,length=186861>
  169. ##contig=<ID=chrUn_gl000223,length=180455>
  170. ##contig=<ID=chrUn_gl000224,length=179693>
  171. ##contig=<ID=chrUn_gl000225,length=211173>
  172. ##contig=<ID=chrUn_gl000226,length=15008>
  173. ##contig=<ID=chrUn_gl000227,length=128374>
  174. ##contig=<ID=chrUn_gl000228,length=129120>
  175. ##contig=<ID=chrUn_gl000229,length=19913>
  176. ##contig=<ID=chrUn_gl000230,length=43691>
  177. ##contig=<ID=chrUn_gl000231,length=27386>
  178. ##contig=<ID=chrUn_gl000232,length=40652>
  179. ##contig=<ID=chrUn_gl000233,length=45941>
  180. ##contig=<ID=chrUn_gl000234,length=40531>
  181. ##contig=<ID=chrUn_gl000235,length=34474>
  182. ##contig=<ID=chrUn_gl000236,length=41934>
  183. ##contig=<ID=chrUn_gl000237,length=45867>
  184. ##contig=<ID=chrUn_gl000238,length=39939>
  185. ##contig=<ID=chrUn_gl000239,length=33824>
  186. ##contig=<ID=chrUn_gl000240,length=41933>
  187. ##contig=<ID=chrUn_gl000241,length=42152>
  188. ##contig=<ID=chrUn_gl000242,length=43523>
  189. ##contig=<ID=chrUn_gl000243,length=43341>
  190. ##contig=<ID=chrUn_gl000244,length=39929>
  191. ##contig=<ID=chrUn_gl000245,length=36651>
  192. ##contig=<ID=chrUn_gl000246,length=38154>
  193. ##contig=<ID=chrUn_gl000247,length=36422>
  194. ##contig=<ID=chrUn_gl000248,length=39786>
  195. ##contig=<ID=chrUn_gl000249,length=38502>
  196. ##contig=<ID=chrEBV,length=171823>
  197. ##reference=file:///data/annos/grch37.p13/grch37.p13.fa
  198. ##bcftools_viewVersion=1.2+htslib-1.2.1
  199. ##bcftools_viewCommand=view -s sy244pa sy244.recalibrated_variants.vcf.gz
  200. ##bcftools_viewCommand=view -i 'FORMAT/GT !~ "[.0]/[.0]"' -o sy244pa.recalibrated_variants.vcf.gz -O z
  201. ##VEP=v85 cache=/data/annos/ensemble/vep_cache/homo_sapiens/86_GRCh37 db=homo_sapiens_core_85_37@ensembldb.ensembl.org HGMD-PUBLIC=20152 ClinVar=201507 ESP=20141103 genebuild=2011-04 regbuild=13 polyphen=2.2.2 sift=sift5.2.2 gencode=GENCODE 19 COSMIC=71 assembly=GRCh37.p13 dbSNP=144
  202. ##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|VARIANT_CLASS|MINIMISED|SYMBOL_SOURCE|HGNC_ID|CCDS|GENE_PHENO|SIFT|PolyPhen|GMAF|AFR_MAF|AMR_MAF|EAS_MAF|EUR_MAF|SAS_MAF|AA_MAF|EA_MAF|ExAC_MAF|ExAC_Adj_MAF|ExAC_AFR_MAF|ExAC_AMR_MAF|ExAC_EAS_MAF|ExAC_FIN_MAF|ExAC_NFE_MAF|ExAC_OTH_MAF|ExAC_SAS_MAF|FREQS|CLIN_SIG|SOMATIC|PHENO|PUBMED|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE">
  203. ##bcftools_viewVersion=1.3.1+htslib-1.3.1
  204. ##bcftools_viewCommand=view -h /archive/sample_data/sy244/sy244pa.recalibrated_variants_vep.vcf.gz
  205. #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sy244pa
  206. chr1 46084614 . C CTTT,CTTTT 2365.77 PASS AC=1,1;AF=0.5,0.5;AN=2;DP=59;FS=0;MLEAC=1,1;MLEAF=0.5,0.5;MQ=60;QD=29.85;SOR=1.238;VQSLOD=4.73;culprit=FS;CSQ=TTT|downstream_gene_variant|MODIFIER|CCDC17|ENSG00000159588|Transcript|ENST00000343901|protein_coding||||||||||rs35220217|1102|-1||insertion||HGNC|26574||||||||||||||||||||||||||||||,TTTT|downstream_gene_variant|MODIFIER|CCDC17|ENSG00000159588|Transcript|ENST00000343901|protein_coding||||||||||rs35220217|1102|-1||insertion||HGNC|26574||||||||||||||||||||||||||||||,TTT|downstream_gene_variant|MODIFIER|NASP|ENSG00000132780|Transcript|ENST00000350030|protein_coding||||||||||rs35220217|48|1||insertion||HGNC|7644|CCDS524.1|||||||||||||||||||||||||||||,TTTT|downstream_gene_variant|MODIFIER|NASP|ENSG00000132780|Transcript|ENST00000350030|protein_coding||||||||||rs35220217|48|1||insertion||HGNC|7644|CCDS524.1|||||||||||||||||||||||||||||,TTT|downstream_gene_variant|MODIFIER|NASP|ENSG00000132780|Transcript|ENST00000351223|protein_coding||||||||||rs35220217|695|1||insertion||HGNC|7644|CCDS525.1|||||||||||||||||||||||||||||,TTTT|downstream_gene_variant|MODIFIER|NASP|ENSG00000132780|Transcript|ENST00000351223|protein_coding||||||||||rs35220217|695|1||insertion||HGNC|7644|CCDS525.1|||||||||||||||||||||||||||||,TTT|downstream_gene_variant|MODIFIER|CCDC17|ENSG00000159588|Transcript|ENST00000372044|nonsense_mediated_decay||||||||||rs35220217|1101|-1||insertion||HGNC|26574||||||||||||||||||||||||||||||,TTTT|downstream_gene_variant|MODIFIER|CCDC17|ENSG00000159588|Transcript|ENST00000372044|nonsense_mediated_decay||||||||||rs35220217|1101|-1||insertion||HGNC|26574||||||||||||||||||||||||||||||,TTT|downstream_gene_variant|MODIFIER|NASP|ENSG00000132780|Transcript|ENST00000372052|protein_coding||||||||||rs35220217|696|1||insertion||HGNC|7644||||||||||||||||||||||||||||||,TTTT|downstream_gene_variant|MODIFIER|NASP|ENSG00000132780|Transcript|ENST00000372052|protein_coding||||||||||rs35220217|696|1||insertion||HGNC|7644||||||||||||||||||||||||||||||,TTT|downstream_gene_variant|MODIFIER|NASP|ENSG00000132780|Transcript|ENST00000402363|protein_coding||||||||||rs35220217|698|1||insertion||HGNC|7644||||||||||||||||||||||||||||||,TTTT|downstream_gene_variant|MODIFIER|NASP|ENSG00000132780|Transcript|ENST00000402363|protein_coding||||||||||rs35220217|698|1||insertion||HGNC|7644||||||||||||||||||||||||||||||,TTT|downstream_gene_variant|MODIFIER|CCDC17|ENSG00000159588|Transcript|ENST00000421127|protein_coding||||||||||rs35220217|1102|-1||insertion||HGNC|26574|CCDS53314.1|||||||||||||||||||||||||||||,TTTT|downstream_gene_variant|MODIFIER|CCDC17|ENSG00000159588|Transcript|ENST00000421127|protein_coding||||||||||rs35220217|1102|-1||insertion||HGNC|26574|CCDS53314.1|||||||||||||||||||||||||||||,TTT|downstream_gene_variant|MODIFIER|NASP|ENSG00000132780|Transcript|ENST00000437362|nonsense_mediated_decay||||||||||rs35220217|3811|1||insertion||HGNC|7644||||||||||||||||||||||||||||||,TTTT|downstream_gene_variant|MODIFIER|NASP|ENSG00000132780|Transcript|ENST00000437362|nonsense_mediated_decay||||||||||rs35220217|3811|1||insertion||HGNC|7644||||||||||||||||||||||||||||||,TTT|downstream_gene_variant|MODIFIER|NASP|ENSG00000132780|Transcript|ENST00000437901|protein_coding||||||||||rs35220217|3811|1|cds_end_NF|insertion||HGNC|7644||||||||||||||||||||||||||||||,TTTT|downstream_gene_variant|MODIFIER|NASP|ENSG00000132780|Transcript|ENST00000437901|protein_coding||||||||||rs35220217|3811|1|cds_end_NF|insertion||HGNC|7644||||||||||||||||||||||||||||||,TTT|downstream_gene_variant|MODIFIER|CCDC17|ENSG00000159588|Transcript|ENST00000445048|protein_coding||||||||||rs35220217|1280|-1||insertion||HGNC|26574||||||||||||||||||||||||||||||,TTTT|downstream_gene_variant|MODIFIER|CCDC17|ENSG00000159588|Transcript|ENST00000445048|protein_coding||||||||||rs35220217|1280|-1||insertion||HGNC|26574||||||||||||||||||||||||||||||,TTT|downstream_gene_variant|MODIFIER|NASP|ENSG00000132780|Transcript|ENST00000453748|nonsense_mediated_decay||||||||||rs35220217|3588|1||insertion||HGNC|7644||||||||||||||||||||||||||||||,TTTT|downstream_gene_variant|MODIFIER|NASP|ENSG00000132780|Transcript|ENST00000453748|nonsense_mediated_decay||||||||||rs35220217|3588|1||insertion||HGNC|7644||||||||||||||||||||||||||||||,TTT|downstream_gene_variant|MODIFIER|CCDC17|ENSG00000159588|Transcript|ENST00000464739|processed_transcript||||||||||rs35220217|2051|-1||insertion||HGNC|26574||||||||||||||||||||||||||||||,TTTT|downstream_gene_variant|MODIFIER|CCDC17|ENSG00000159588|Transcript|ENST00000464739|processed_transcript||||||||||rs35220217|2051|-1||insertion||HGNC|26574||||||||||||||||||||||||||||||,TTT|downstream_gene_variant|MODIFIER|NASP|ENSG00000132780|Transcript|ENST00000472408|retained_intron||||||||||rs35220217|696|1||insertion||HGNC|7644||||||||||||||||||||||||||||||,TTTT|downstream_gene_variant|MODIFIER|NASP|ENSG00000132780|Transcript|ENST00000472408|retained_intron||||||||||rs35220217|696|1||insertion||HGNC|7644||||||||||||||||||||||||||||||,TTT|downstream_gene_variant|MODIFIER|CCDC17|ENSG00000159588|Transcript|ENST00000479529|nonsense_mediated_decay||||||||||rs35220217|1410|-1||insertion||HGNC|26574||||||||||||||||||||||||||||||,TTTT|downstream_gene_variant|MODIFIER|CCDC17|ENSG00000159588|Transcript|ENST00000479529|nonsense_mediated_decay||||||||||rs35220217|1410|-1||insertion||HGNC|26574||||||||||||||||||||||||||||||,TTT|downstream_gene_variant|MODIFIER|NASP|ENSG00000132780|Transcript|ENST00000481782|retained_intron||||||||||rs35220217|698|1||insertion||HGNC|7644||||||||||||||||||||||||||||||,TTTT|downstream_gene_variant|MODIFIER|NASP|ENSG00000132780|Transcript|ENST00000481782|retained_intron||||||||||rs35220217|698|1||insertion||HGNC|7644||||||||||||||||||||||||||||||,TTT|downstream_gene_variant|MODIFIER|CCDC17|ENSG00000159588|Transcript|ENST00000482416|retained_intron||||||||||rs35220217|1101|-1||insertion||HGNC|26574||||||||||||||||||||||||||||||,TTTT|downstream_gene_variant|MODIFIER|CCDC17|ENSG00000159588|Transcript|ENST00000482416|retained_intron||||||||||rs35220217|1101|-1||insertion||HGNC|26574||||||||||||||||||||||||||||||,TTT|downstream_gene_variant|MODIFIER|CCDC17|ENSG00000159588|Transcript|ENST00000491755|retained_intron||||||||||rs35220217|1101|-1||insertion||HGNC|26574||||||||||||||||||||||||||||||,TTTT|downstream_gene_variant|MODIFIER|CCDC17|ENSG00000159588|Transcript|ENST00000491755|retained_intron||||||||||rs35220217|1101|-1||insertion||HGNC|26574||||||||||||||||||||||||||||||,TTT|downstream_gene_variant|MODIFIER|NASP|ENSG00000132780|Transcript|ENST00000525515|protein_coding||||||||||rs35220217|4825|1|cds_end_NF|insertion||HGNC|7644||||||||||||||||||||||||||||||,TTTT|downstream_gene_variant|MODIFIER|NASP|ENSG00000132780|Transcript|ENST00000525515|protein_coding||||||||||rs35220217|4825|1|cds_end_NF|insertion||HGNC|7644||||||||||||||||||||||||||||||,TTT|downstream_gene_variant|MODIFIER|CCDC17|ENSG00000159588|Transcript|ENST00000525599|retained_intron||||||||||rs35220217|3338|-1||insertion||HGNC|26574||||||||||||||||||||||||||||||,TTTT|downstream_gene_variant|MODIFIER|CCDC17|ENSG00000159588|Transcript|ENST00000525599|retained_intron||||||||||rs35220217|3338|-1||insertion||HGNC|26574||||||||||||||||||||||||||||||,TTT|downstream_gene_variant|MODIFIER|NASP|ENSG00000132780|Transcript|ENST00000527359|nonsense_mediated_decay||||||||||rs35220217|3536|1||insertion||HGNC|7644||||||||||||||||||||||||||||||,TTTT|downstream_gene_variant|MODIFIER|NASP|ENSG00000132780|Transcript|ENST00000527359|nonsense_mediated_decay||||||||||rs35220217|3536|1||insertion||HGNC|7644||||||||||||||||||||||||||||||,TTT|downstream_gene_variant|MODIFIER|NASP|ENSG00000132780|Transcript|ENST00000527932|retained_intron||||||||||rs35220217|3227|1||insertion||HGNC|7644||||||||||||||||||||||||||||||,TTTT|downstream_gene_variant|MODIFIER|NASP|ENSG00000132780|Transcript|ENST00000527932|retained_intron||||||||||rs35220217|3227|1||insertion||HGNC|7644||||||||||||||||||||||||||||||,TTT|downstream_gene_variant|MODIFIER|NASP|ENSG00000132780|Transcript|ENST00000528238|protein_coding||||||||||rs35220217|3479|1|cds_end_NF|insertion||HGNC|7644||||||||||||||||||||||||||||||,TTTT|downstream_gene_variant|MODIFIER|NASP|ENSG00000132780|Transcript|ENST00000528238|protein_coding||||||||||rs35220217|3479|1|cds_end_NF|insertion||HGNC|7644||||||||||||||||||||||||||||||,TTT|downstream_gene_variant|MODIFIER|CCDC17|ENSG00000159588|Transcript|ENST00000528266|protein_coding||||||||||rs35220217|1168|-1||insertion||HGNC|26574|CCDS44131.2|||||||||||||||||||||||||||||,TTTT|downstream_gene_variant|MODIFIER|CCDC17|ENSG00000159588|Transcript|ENST00000528266|protein_coding||||||||||rs35220217|1168|-1||insertion||HGNC|26574|CCDS44131.2|||||||||||||||||||||||||||||,TTT|downstream_gene_variant|MODIFIER|NASP|ENSG00000132780|Transcript|ENST00000530073|processed_transcript||||||||||rs35220217|698|1||insertion||HGNC|7644||||||||||||||||||||||||||||||,TTTT|downstream_gene_variant|MODIFIER|NASP|ENSG00000132780|Transcript|ENST00000530073|processed_transcript||||||||||rs35220217|698|1||insertion||HGNC|7644||||||||||||||||||||||||||||||,TTT|downstream_gene_variant|MODIFIER|NASP|ENSG00000132780|Transcript|ENST00000531612|protein_coding||||||||||rs35220217|729|1|cds_start_NF|insertion||HGNC|7644||||||||||||||||||||||||||||||,TTTT|downstream_gene_variant|MODIFIER|NASP|ENSG00000132780|Transcript|ENST00000531612|protein_coding||||||||||rs35220217|729|1|cds_start_NF|insertion||HGNC|7644||||||||||||||||||||||||||||||,TTT|downstream_gene_variant|MODIFIER|NASP|ENSG00000132780|Transcript|ENST00000534450|protein_coding||||||||||rs35220217|695|1|cds_start_NF|insertion||HGNC|7644||||||||||||||||||||||||||||||,TTTT|downstream_gene_variant|MODIFIER|NASP|ENSG00000132780|Transcript|ENST00000534450|protein_coding||||||||||rs35220217|695|1|cds_start_NF|insertion||HGNC|7644||||||||||||||||||||||||||||||,TTT|downstream_gene_variant|MODIFIER|NASP|ENSG00000132780|Transcript|ENST00000537798|protein_coding||||||||||rs35220217|691|1||insertion||HGNC|7644|CCDS55597.1|||||||||||||||||||||||||||||,TTTT|downstream_gene_variant|MODIFIER|NASP|ENSG00000132780|Transcript|ENST00000537798|protein_coding||||||||||rs35220217|691|1||insertion||HGNC|7644|CCDS55597.1||||||||||||||||||||||||||||| GT:AD:DP:GQ:PL 1/2:0,25,32:57:99:2394,909,741,642,0,472
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