70 lines
14 KiB
Plaintext
70 lines
14 KiB
Plaintext
##fileformat=VCFv4.0
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##ALT=<ID=DEL,Description="Deletion">
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##FILTER=<ID=COHERENCE,Description="GSCOHPVALUE == "NA" || GSCOHPVALUE <= 0.01">
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##FILTER=<ID=COVERAGE,Description="GSDEPTHCALLTHRESHOLD == "NA" || GSDEPTHCALLTHRESHOLD >= 1.0">
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##FILTER=<ID=DEPTH,Description="GSDEPTHRATIO == "NA" || GSDEPTHRATIO > 0.8 || (GSDEPTHRATIO > 0.63 && (GSMEMBPVALUE == "NA" || GSMEMBPVALUE >= 0.01))">
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##FILTER=<ID=DEPTHPVAL,Description="GSDEPTHPVALUE == "NA" || GSDEPTHPVALUE >= 0.01">
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##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events">
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##FORMAT=<ID=CNL,Number=.,Type=Float,Description="Copy number likelihoods">
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##FORMAT=<ID=CNQ,Number=1,Type=Float,Description="Copy number genotype quality for imprecise events">
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##FORMAT=<ID=GL,Number=.,Type=Float,Description="Genotype likelihoods">
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##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype quality">
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##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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##FORMAT=<ID=PL,Number=.,Type=Integer,Description="Genotype phred likelihoods">
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##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
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##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
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##INFO=<ID=END,Number=1,Type=Integer,Description="End coordinate of this variant">
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##INFO=<ID=GSCOHERENCE,Number=1,Type=Float,Description="Value of coherence statistic">
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##INFO=<ID=GSCOHFN,Number=1,Type=Float,Description="Coherence statistic per pair">
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##INFO=<ID=GSCOHPVALUE,Number=1,Type=Float,Description="Coherence metric (not a true p-value)">
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##INFO=<ID=GSCOORDS,Number=4,Type=Integer,Description="Original cluster coordinates">
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##INFO=<ID=GSCORA6,Number=1,Type=Float,Description="Correlation with array intensity from Affy6 arrays">
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##INFO=<ID=GSCORI1M,Number=1,Type=Float,Description="Correlation with array intensity from Illumina 1M arrays">
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##INFO=<ID=GSCORNG,Number=1,Type=Float,Description="Correlation with array intensity from NimbleGen arrays">
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##INFO=<ID=GSDEPTHCALLS,Number=.,Type=String,Description="Samples with discrepant read pairs or low read depth">
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##INFO=<ID=GSDEPTHCALLTHRESHOLD,Number=1,Type=Float,Description="Read depth threshold (median read depth of samples with discrepant read pairs)">
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##INFO=<ID=GSDEPTHNOBSSAMPLES,Number=1,Type=Integer,Description="Number of samples with discrepant read pairs in depth test">
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##INFO=<ID=GSDEPTHNTOTALSAMPLES,Number=1,Type=Integer,Description="Total samples in depth test">
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##INFO=<ID=GSDEPTHOBSSAMPLES,Number=.,Type=String,Description="Samples with discrepant read pairs in depth test">
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##INFO=<ID=GSDEPTHPVALUE,Number=1,Type=Float,Description="Depth p-value using chi-squared test">
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##INFO=<ID=GSDEPTHPVALUECOUNTS,Number=4,Type=Integer,Description="Depth test read counts (carrier inside event, carrier outside event, non-carrier inside, non-carrier outside)">
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##INFO=<ID=GSDEPTHRANKSUMPVALUE,Number=1,Type=Float,Description="Depth p-value using rank-sum test">
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##INFO=<ID=GSDEPTHRATIO,Number=1,Type=Float,Description="Read depth ratio test">
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##INFO=<ID=GSDMAX,Number=1,Type=Integer,Description="Maximum value considered for DOpt">
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##INFO=<ID=GSDMIN,Number=1,Type=Integer,Description="Minimum value considered for DOpt">
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##INFO=<ID=GSDOPT,Number=1,Type=Integer,Description="Most likely event length">
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##INFO=<ID=GSDSPAN,Number=1,Type=Integer,Description="Inner span length of read pair cluster">
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##INFO=<ID=GSELENGTH,Number=1,Type=Integer,Description="Original cluster coordinates">
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##INFO=<ID=GSMEMBNPAIRS,Number=1,Type=Integer,Description="Number of pairs used in membership test">
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##INFO=<ID=GSMEMBNSAMPLES,Number=1,Type=Integer,Description="Number of samples used in membership test">
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##INFO=<ID=GSMEMBOBSSAMPLES,Number=.,Type=String,Description="Samples participating in membership test">
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##INFO=<ID=GSMEMBPVALUE,Number=1,Type=Float,Description="Membership p-value">
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##INFO=<ID=GSMEMBSTATISTIC,Number=1,Type=Float,Description="Value of membership statistic">
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##INFO=<ID=GSNDEPTHCALLS,Number=1,Type=Integer,Description="Number of samples with discrepant read pairs or low read depth">
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##INFO=<ID=GSNHET,Number=1,Type=Integer,Description="Number of heterozygous snp genotype calls inside the event">
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##INFO=<ID=GSNHOM,Number=1,Type=Integer,Description="Number of homozygous snp genotype calls inside the event">
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##INFO=<ID=GSNNOCALL,Number=1,Type=Integer,Description="Number of snp genotype non-calls inside the event">
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##INFO=<ID=GSNPAIRS,Number=1,Type=Integer,Description="Number of discrepant read pairs">
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##INFO=<ID=GSNSAMPLES,Number=1,Type=Integer,Description="Number of samples with discrepant read pairs">
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##INFO=<ID=GSNSNPS,Number=1,Type=Integer,Description="Number of snps inside the event">
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##INFO=<ID=GSOUTLEFT,Number=1,Type=Integer,Description="Number of outlier read pairs on left">
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##INFO=<ID=GSOUTLIERS,Number=1,Type=Integer,Description="Number of outlier read pairs">
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##INFO=<ID=GSOUTRIGHT,Number=1,Type=Integer,Description="Number of outlier read pairs on right">
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##INFO=<ID=GSREADGROUPS,Number=.,Type=String,Description="Read groups contributing discrepant read pairs">
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##INFO=<ID=GSREADNAMES,Number=.,Type=String,Description="Discrepant read pair identifiers">
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##INFO=<ID=GSSAMPLES,Number=.,Type=String,Description="Samples contributing discrepant read pairs">
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##INFO=<ID=GSSNPHET,Number=1,Type=Float,Description="Fraction of het snp genotype calls inside the event">
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##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
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##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
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##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
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##INFO=<ID=NOVEL,Number=0,Type=Flag,Description="Indicates a novel structural variation">
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##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
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##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
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##VariantFiltration="analysis_type=VariantFiltration input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=data/human_b36_chr1.fasta rodBind=[test1/test1.discovery.unfiltered.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub filterExpression=[GSDEPTHCALLTHRESHOLD == "NA" || GSDEPTHCALLTHRESHOLD >= 1.0, GSCOHPVALUE == "NA" || GSCOHPVALUE <= 0.01, GSDEPTHPVALUE == "NA" || GSDEPTHPVALUE >= 0.01, GSDEPTHRATIO == "NA" || GSDEPTHRATIO > 0.8 || (GSDEPTHRATIO > 0.63 && (GSMEMBPVALUE == "NA" || GSMEMBPVALUE >= 0.01))] filterName=[COVERAGE, COHERENCE, DEPTHPVAL, DEPTH] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskExtension=0 maskName=Mask missingValuesInExpressionsShouldEvaluateAsFailing=false"
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#CHROM POS ID REF ALT QUAL FILTER INFO
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1 61722559 DEL_1 T <DEL> . DEPTH;DEPTHPVAL CIEND=-8,8;CIPOS=-8,8;END=61722981;GSCOHERENCE=-3.1627112805546047;GSCOHFN=-0.5271185467591007;GSCOHPVALUE=0.901;GSCOORDS=61722491,61722556,61723000,61723144;GSDEPTHCALLTHRESHOLD=0.9600579875024452;GSDEPTHNOBSSAMPLES=5;GSDEPTHNTOTALSAMPLES=5;GSDEPTHOBSSAMPLES=NA07051,NA11830,NA11920,NA12003,NA12249;GSDEPTHPVALUE=0.035631;GSDEPTHPVALUECOUNTS=74,35512,511,321039;GSDEPTHRANKSUMPVALUE=0.9802336;GSDEPTHRATIO=1.3091622731975827;GSDMAX=543;GSDMIN=1;GSDOPT=420;GSDSPAN=443;GSMEMBNPAIRS=6;GSMEMBNSAMPLES=5;GSMEMBOBSSAMPLES=NA07051,NA12249,NA11920,NA12003,NA11830;GSMEMBPVALUE=0.4945;GSMEMBSTATISTIC=40.43627779276575;GSNDEPTHCALLS=39;GSNPAIRS=6;GSNSAMPLES=5;GSOUTLEFT=0;GSOUTLIERS=0;GSOUTRIGHT=0;GSREADGROUPS=ERR000550,ERR000567,SRR003115,SRR003135,SRR006095,SRR006165;GSREADNAMES=EAS139_44:6:82:100:15931,EAS139_47:7:5:530:8011,SRR003115.6626735,SRR003135.5278653,SRR006095.2235470,SRR006165.7774794;GSSAMPLES=NA07051,NA12249,NA11920,NA12003,NA11830,NA07051;IMPRECISE;SVLEN=-420;SVTYPE=DEL
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1 61748746 DEL_2 C <DEL> . COVERAGE;DEPTH;DEPTHPVAL CIEND=-10,10;CIPOS=-10,10;END=61748911;GSCOHERENCE=-1.4443037653483857;GSCOHFN=-0.7221518826741928;GSCOHPVALUE=0.5759;GSCOORDS=61748632,61748738,61748939,61749061;GSDEPTHCALLTHRESHOLD=1.2071639891989663;GSDEPTHNOBSSAMPLES=2;GSDEPTHNTOTALSAMPLES=2;GSDEPTHOBSSAMPLES=NA11919,NA12155;GSDEPTHPVALUE=0.961576;GSDEPTHPVALUECOUNTS=16,12443,423,344254;GSDEPTHRANKSUMPVALUE=0.5871828;GSDEPTHRATIO=1.046486208790572;GSDMAX=300;GSDMIN=1;GSDOPT=163;GSDSPAN=200;GSMEMBNPAIRS=2;GSMEMBNSAMPLES=2;GSMEMBOBSSAMPLES=NA12155,NA11919;GSMEMBPVALUE=0.1092;GSMEMBSTATISTIC=62.062109599506876;GSNDEPTHCALLS=25;GSNPAIRS=2;GSNSAMPLES=2;GSOUTLEFT=0;GSOUTLIERS=0;GSOUTRIGHT=0;GSREADGROUPS=SRR003124,SRR006158;GSREADNAMES=SRR003124.4475171,SRR006158.14034222;GSSAMPLES=NA12155,NA11919;IMPRECISE;SVLEN=-163;SVTYPE=DEL
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1 61855447 DEL_3 T <DEL> . PASS CIEND=0,1;CIPOS=0,1;END=61856292;GSCOHERENCE=-52.00960064852534;GSCOHFN=-1.040192012970507;GSCOHPVALUE=0.3629;GSCOORDS=61855215,61855454,61856287,61856521;GSDEPTHCALLTHRESHOLD=0.5590142042896722;GSDEPTHNOBSSAMPLES=22;GSDEPTHNTOTALSAMPLES=22;GSDEPTHOBSSAMPLES=NA06986,NA07037,NA07346,NA07347,NA07357,NA11829,NA11831,NA11881,NA11918,NA11920,NA11993,NA12006,NA12144,NA12154,NA12249,NA12287,NA12489,NA12716,NA12751,NA12761,NA12776,NA12828;GSDEPTHPVALUE=0.0;GSDEPTHPVALUECOUNTS=330,164872,985,190949;GSDEPTHRANKSUMPVALUE=4.153498E-8;GSDEPTHRATIO=0.38801471093526974;GSDMAX=932;GSDMIN=1;GSDOPT=845;GSDSPAN=832;GSMEMBNPAIRS=53;GSMEMBNSAMPLES=22;GSMEMBOBSSAMPLES=NA12249,NA12761,NA12751,NA12716,NA07357,NA07037,NA12489,NA11993,NA12287,NA11881,NA12006,NA12776,NA12144,NA12828,NA11920,NA11918,NA06986,NA07347,NA11831,NA12154,NA07346,NA11829;GSMEMBPVALUE=1.0E-4;GSMEMBSTATISTIC=104.20398691850474;GSNDEPTHCALLS=23;GSNPAIRS=53;GSNSAMPLES=22;GSOUTLEFT=2;GSOUTLIERS=3;GSOUTRIGHT=1;GSREADGROUPS=ERR000561,ERR000601,ERR000603,ERR000603,ERR000605,ERR000608,ERR000608,ERR000594,ERR000597,ERR000599,ERR000569,ERR000575,ERR001458,ERR001458,ERR001460,ERR001463,ERR001512,ERR001563,ERR002150,ERR000768,ERR000850,ERR000852,ERR000855,ERR000721,ERR000748,ERR002358,ERR002307,ERR002311,ERR002313,ERR000937,ERR000956,ERR000760,ERR001694,SRR003117,SRR003436,SRR003667,SRR003671,SRR006019,SRR006118,SRR006119,SRR006135,SRR006142,SRR006142,SRR006170,SRR006172,SRR011017,SRR011021,SRR011026,SRR011033,SRR011036,SRR011045,SRR011055,SRR011073;GSREADNAMES=EAS139_47:1:25:1471:14551,EAS188_47:1:75:1331:16391,EAS188_47:3:1:1216:4151,EAS188_47:3:95:1166:18591,EAS188_47:5:16:565:11781,EAS188_47:8:31:1573:16981,EAS188_47:8:92:1045:13491,EAS188_49:2:27:392:1221,EAS188_49:5:32:781:7701,EAS188_49:7:52:1693:8851,EAS254_17:1:44:1615:13131,EAS254_17:7:96:1501:971,ERR001458.1511982,ERR001458.6912307,ERR001460.5480400,ERR001463.463921,ERR001512.508584,ERR001563.5329559,IL11_651:3:80:915:572,IL14_915:3:85:615:6201,IL16_822:1:225:719:9121,IL16_822:3:148:350:3722,IL16_822:7:157:639:9591,IL18_838:5:24:450:5962,IL22_934:3:170:971:5961,IL25_518:2:127:200:580,IL27_543:1:85:977:136,IL27_543:6:180:493:195,IL27_543:8:147:633:373,IL5_951:7:154:581:4601,IL6_1091:5:108:170:3761,IL8_955:2:188:668:4051,IL9_498:5:289:365:17,SRR003117.5014249,SRR003436.5792642,SRR003667.8059832,SRR003671.12611793,SRR006019.3905547,SRR006118.11717525,SRR006119.10119087,SRR006135.5824743,SRR006142.10638045,SRR006142.9562721,SRR006170.1365044,SRR006172.5017613,SRR011017.7961919,SRR011021.4733388,SRR011026.7635354,SRR011033.4403290,SRR011036.5505112,SRR011045.6651532,SRR011055.526762,SRR011073.1259706;GSSAMPLES=NA12249,NA12761,NA12761,NA12761,NA12761,NA12761,NA12761,NA12751,NA12751,NA12751,NA12716,NA12716,NA07357,NA07357,NA07357,NA07357,NA07357,NA07037,NA12489,NA11993,NA12287,NA12287,NA12287,NA12287,NA11881,NA12006,NA12776,NA12776,NA12776,NA12144,NA12006,NA12144,NA12828,NA11920,NA11918,NA06986,NA06986,NA07347,NA11831,NA11831,NA12154,NA06986,NA06986,NA07346,NA11829,NA11831,NA11831,NA11829,NA12154,NA12154,NA07346,NA07347,NA07346;IMPRECISE;SVLEN=-845;SVTYPE=DEL
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1 61886011 DEL_4 A <DEL> . PASS CIEND=-6,6;CIPOS=-6,6;END=61892126;GSCOHERENCE=-11.434559556981338;GSCOHFN=-0.9528799630817781;GSCOHPVALUE=0.521;GSCOORDS=61885841,61886006,61892143,61892283;GSDEPTHCALLTHRESHOLD=0.47598136818532377;GSDEPTHNOBSSAMPLES=7;GSDEPTHNTOTALSAMPLES=7;GSDEPTHOBSSAMPLES=NA07357,NA11829,NA11831,NA12003,NA12155,NA12249,NA12750;GSDEPTHPVALUE=0.0;GSDEPTHPVALUECOUNTS=730,48671,8012,299723;GSDEPTHRANKSUMPVALUE=7.009347E-4;GSDEPTHRATIO=0.5610889566494703;GSDMAX=6236;GSDMIN=5237;GSDOPT=6113;GSDSPAN=6136;GSMEMBNPAIRS=12;GSMEMBNSAMPLES=7;GSMEMBOBSSAMPLES=NA12750,NA12249,NA07357,NA12155,NA12003,NA11831,NA11829;GSMEMBPVALUE=0.0022;GSMEMBSTATISTIC=88.21331161391709;GSNDEPTHCALLS=11;GSNPAIRS=12;GSNSAMPLES=7;GSOUTLEFT=0;GSOUTLIERS=0;GSOUTRIGHT=0;GSREADGROUPS=ERR000587,ERR000561,ERR000562,ERR000563,ERR000564,ERR001458,SRR003124,SRR003133,SRR003135,SRR006119,SRR011026,SRR011026;GSREADNAMES=EAS139_45:3:82:970:10791,EAS139_47:1:57:1702:451,EAS139_47:2:9:1374:11191,EAS139_47:3:68:1258:15071,EAS139_47:4:65:960:8761,ERR001458.3398233,SRR003124.3412979,SRR003133.672892,SRR003135.3714244,SRR006119.5864265,SRR011026.3160375,SRR011026.6471234;GSSAMPLES=NA12750,NA12249,NA12249,NA12249,NA12249,NA07357,NA12155,NA12003,NA12003,NA11831,NA11829,NA11829;IMPRECISE;SVLEN=-6113;SVTYPE=DEL
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1 61892838 DEL_5 G <DEL> . PASS CIEND=-24,25;CIPOS=-24,25;END=61893006;GSCOHERENCE=-1.9466175377489223;GSCOHFN=-0.9733087688744612;GSCOHPVALUE=0.424;GSCOORDS=61892760,61892812,61893082,61893133;GSDEPTHCALLTHRESHOLD=0.044234556389327793;GSDEPTHNOBSSAMPLES=2;GSDEPTHNTOTALSAMPLES=2;GSDEPTHOBSSAMPLES=NA11919,NA12155;GSDEPTHPVALUE=1.15E-4;GSDEPTHPVALUECOUNTS=1,12458,492,344185;GSDEPTHRANKSUMPVALUE=0.00893578;GSDEPTHRATIO=0.056153717139996895;GSDMAX=369;GSDMIN=1;GSDOPT=166;GSDSPAN=269;GSMEMBNPAIRS=2;GSMEMBNSAMPLES=2;GSMEMBOBSSAMPLES=NA12155,NA11919;GSMEMBPVALUE=0.1092;GSMEMBSTATISTIC=62.062109599506876;GSNDEPTHCALLS=2;GSNPAIRS=2;GSNSAMPLES=2;GSOUTLEFT=0;GSOUTLIERS=0;GSOUTRIGHT=0;GSREADGROUPS=SRR003123,SRR006158;GSREADNAMES=SRR003123.2623325,SRR006158.13888082;GSSAMPLES=NA12155,NA11919;IMPRECISE;SVLEN=-166;SVTYPE=DEL
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