1##fileformat=VCFv4.2 2##Biotin(Bgnd)=Biotin(Bgnd)|Staining|508|179 3##Biotin(High)=Biotin(High)|Staining|778|5902 4##DNP(Bgnd)=DNP(Bgnd)|Staining|1058|245 5##DNP(High)=DNP(High)|Staining|32198|156 6##Extension(A)=Extension(A)|Extension|41089|480 7##Extension(C)=Extension(C)|Extension|2446|11515 8##Extension(G)=Extension(G)|Extension|2936|11197 9##Extension(T)=Extension(T)|Extension|43350|395 10##FILTER=<ID=DUPE,Description="Duplicate assays position."> 11##FILTER=<ID=FAIL_REF,Description="Assay failed to map to reference."> 12##FILTER=<ID=TRIALLELIC,Description="Tri-allelic assay."> 13##FILTER=<ID=ZCALL_DIFF,Description="ZCALL_DIFF"> 14##FORMAT=<ID=BAF,Number=1,Type=Float,Description="B Allele Frequency"> 15##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 16##FORMAT=<ID=GTA,Number=1,Type=String,Description="Illumina Autocall Genotype"> 17##FORMAT=<ID=GTZ,Number=1,Type=String,Description="zCall Genotype"> 18##FORMAT=<ID=IGC,Number=1,Type=Float,Description="Illumina GenCall Confidence Score"> 19##FORMAT=<ID=LRR,Number=1,Type=Float,Description="Log R Ratio"> 20##FORMAT=<ID=NORMX,Number=1,Type=Float,Description="Normalized X intensity"> 21##FORMAT=<ID=NORMY,Number=1,Type=Float,Description="Normalized Y intensity"> 22##FORMAT=<ID=R,Number=1,Type=Float,Description="Normalized R value"> 23##FORMAT=<ID=THETA,Number=1,Type=Float,Description="Normalized Theta value"> 24##FORMAT=<ID=X,Number=1,Type=Integer,Description="Raw X intensity"> 25##FORMAT=<ID=Y,Number=1,Type=Integer,Description="Raw Y intensity"> 26##Hyb(High)=Hyb(High)|Hybridization|3310|11184 27##Hyb(Low)=Hyb(Low)|Hybridization|3436|1823 28##Hyb(Medium)=Hyb(Medium)|Hybridization|1307|6426 29##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> 30##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> 31##INFO=<ID=ALLELE_A,Number=1,Type=String,Description="A allele"> 32##INFO=<ID=ALLELE_B,Number=1,Type=String,Description="B allele"> 33##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> 34##INFO=<ID=BEADSET_ID,Number=1,Type=Integer,Description="Bead set ID for normalization"> 35##INFO=<ID=GC_SCORE,Number=1,Type=Float,Description="Gentrain Score"> 36##INFO=<ID=ILLUMINA_BUILD,Number=1,Type=String,Description="Genome Build in Illumina manifest"> 37##INFO=<ID=ILLUMINA_CHR,Number=1,Type=String,Description="Chromosome in Illumina manifest"> 38##INFO=<ID=ILLUMINA_POS,Number=1,Type=Integer,Description="Position in Illumina manifest"> 39##INFO=<ID=ILLUMINA_STRAND,Number=1,Type=String,Description="Probe strand"> 40##INFO=<ID=N_AA,Number=1,Type=Integer,Description="Number of AA calls in training set"> 41##INFO=<ID=N_AB,Number=1,Type=Integer,Description="Number of AB calls in training set"> 42##INFO=<ID=N_BB,Number=1,Type=Integer,Description="Number of BB calls in training set"> 43##INFO=<ID=PROBE_A,Number=1,Type=String,Description="Probe base pair sequence"> 44##INFO=<ID=PROBE_B,Number=1,Type=String,Description="Probe base pair sequence; not missing for strand-ambiguous SNPs"> 45##INFO=<ID=SOURCE,Number=1,Type=String,Description="Probe source"> 46##INFO=<ID=devR_AA,Number=1,Type=Float,Description="Standard deviation of normalized R for AA cluster"> 47##INFO=<ID=devR_AB,Number=1,Type=Float,Description="Standard deviation of normalized R for AB cluster"> 48##INFO=<ID=devR_BB,Number=1,Type=Float,Description="Standard deviation of normalized R for BB cluster"> 49##INFO=<ID=devTHETA_AA,Number=1,Type=Float,Description="Standard deviation of normalized THETA for AA cluster"> 50##INFO=<ID=devTHETA_AB,Number=1,Type=Float,Description="Standard deviation of normalized THETA for AB cluster"> 51##INFO=<ID=devTHETA_BB,Number=1,Type=Float,Description="Standard deviation of normalized THETA for BB cluster"> 52##INFO=<ID=devX_AA,Number=1,Type=Float,Description="Standard deviation of normalized X for AA cluster"> 53##INFO=<ID=devX_AB,Number=1,Type=Float,Description="Standard deviation of normalized X for AB cluster"> 54##INFO=<ID=devX_BB,Number=1,Type=Float,Description="Standard deviation of normalized X for BB cluster"> 55##INFO=<ID=devY_AA,Number=1,Type=Float,Description="Standard deviation of normalized Y for AA cluster"> 56##INFO=<ID=devY_AB,Number=1,Type=Float,Description="Standard deviation of normalized Y for AB cluster"> 57##INFO=<ID=devY_BB,Number=1,Type=Float,Description="Standard deviation of normalized Y for BB cluster"> 58##INFO=<ID=meanR_AA,Number=1,Type=Float,Description="Mean of normalized R for AA cluster"> 59##INFO=<ID=meanR_AB,Number=1,Type=Float,Description="Mean of normalized R for AB cluster"> 60##INFO=<ID=meanR_BB,Number=1,Type=Float,Description="Mean of normalized R for BB cluster"> 61##INFO=<ID=meanTHETA_AA,Number=1,Type=Float,Description="Mean of normalized THETA for AA cluster"> 62##INFO=<ID=meanTHETA_AB,Number=1,Type=Float,Description="Mean of normalized THETA for AB cluster"> 63##INFO=<ID=meanTHETA_BB,Number=1,Type=Float,Description="Mean of normalized THETA for BB cluster"> 64##INFO=<ID=meanX_AA,Number=1,Type=Float,Description="Mean of normalized X for AA cluster"> 65##INFO=<ID=meanX_AB,Number=1,Type=Float,Description="Mean of normalized X for AB cluster"> 66##INFO=<ID=meanX_BB,Number=1,Type=Float,Description="Mean of normalized X for BB cluster"> 67##INFO=<ID=meanY_AA,Number=1,Type=Float,Description="Mean of normalized Y for AA cluster"> 68##INFO=<ID=meanY_AB,Number=1,Type=Float,Description="Mean of normalized Y for AB cluster"> 69##INFO=<ID=meanY_BB,Number=1,Type=Float,Description="Mean of normalized Y for BB cluster"> 70##INFO=<ID=refSNP,Number=1,Type=String,Description="dbSNP rs ID"> 71##INFO=<ID=zthresh_X,Number=1,Type=Float,Description="zCall X threshold"> 72##INFO=<ID=zthresh_Y,Number=1,Type=Float,Description="zCall Y threshold"> 73##NP(A)=NP(A)|Non-Polymorphic|17148|391 74##NP(C)=NP(C)|Non-Polymorphic|1093|6000 75##NP(G)=NP(G)|Non-Polymorphic|1286|5170 76##NP(T)=NP(T)|Non-Polymorphic|15772|304 77##NSB(Bgnd)Blue=NSB(Bgnd)Blue|Non-SpecificBinding|922|301 78##NSB(Bgnd)Green=NSB(Bgnd)Green|Non-SpecificBinding|842|238 79##NSB(Bgnd)Purple=NSB(Bgnd)Purple|Non-SpecificBinding|912|204 80##NSB(Bgnd)Red=NSB(Bgnd)Red|Non-SpecificBinding|1016|295 81##Restore=Restore|Restoration|961|374 82##String(MM)=String(MM)|Stringency|4768|259 83##String(PM)=String(PM)|Stringency|29830|468 84##TargetRemoval=TargetRemoval|TargetRemoval|2492|281 85##analysisVersionNumber=1 86##arrayType=PsychChip_v1-1_15073391_A1 87##autocallDate=08/17/2017 00:40 88##autocallGender=F 89##autocallVersion=2.0.0.137 90##chipWellBarcode=0816201804HC0_R01C01 91##clusterFile=PsychChip_v1-1_15073391_A1_ClusterFile.egt 92##content=PsychChip_v1-1_15073391_A1.1.2.extended.csv 93##contig=<ID=1,length=249250621,assembly=GRCh37> 94##contig=<ID=2,length=243199373,assembly=GRCh37> 95##contig=<ID=3,length=198022430,assembly=GRCh37> 96##contig=<ID=4,length=191154276,assembly=GRCh37> 97##contig=<ID=5,length=180915260,assembly=GRCh37> 98##contig=<ID=6,length=171115067,assembly=GRCh37> 99##contig=<ID=7,length=159138663,assembly=GRCh37> 100##contig=<ID=8,length=146364022,assembly=GRCh37> 101##contig=<ID=9,length=141213431,assembly=GRCh37> 102##contig=<ID=10,length=135534747,assembly=GRCh37> 103##contig=<ID=11,length=135006516,assembly=GRCh37> 104##contig=<ID=12,length=133851895,assembly=GRCh37> 105##contig=<ID=13,length=115169878,assembly=GRCh37> 106##contig=<ID=14,length=107349540,assembly=GRCh37> 107##contig=<ID=15,length=102531392,assembly=GRCh37> 108##contig=<ID=16,length=90354753,assembly=GRCh37> 109##contig=<ID=17,length=81195210,assembly=GRCh37> 110##contig=<ID=18,length=78077248,assembly=GRCh37> 111##contig=<ID=19,length=59128983,assembly=GRCh37> 112##contig=<ID=20,length=63025520,assembly=GRCh37> 113##contig=<ID=21,length=48129895,assembly=GRCh37> 114##contig=<ID=22,length=51304566,assembly=GRCh37> 115##contig=<ID=X,length=155270560,assembly=GRCh37> 116##contig=<ID=Y,length=59373566,assembly=GRCh37> 117##contig=<ID=MT,length=16569,assembly=GRCh37> 118##contig=<ID=GL000207.1,length=4262,assembly=GRCh37> 119##contig=<ID=GL000226.1,length=15008,assembly=GRCh37> 120##contig=<ID=GL000229.1,length=19913,assembly=GRCh37> 121##contig=<ID=GL000231.1,length=27386,assembly=GRCh37> 122##contig=<ID=GL000210.1,length=27682,assembly=GRCh37> 123##contig=<ID=GL000239.1,length=33824,assembly=GRCh37> 124##contig=<ID=GL000235.1,length=34474,assembly=GRCh37> 125##contig=<ID=GL000201.1,length=36148,assembly=GRCh37> 126##contig=<ID=GL000247.1,length=36422,assembly=GRCh37> 127##contig=<ID=GL000245.1,length=36651,assembly=GRCh37> 128##contig=<ID=GL000197.1,length=37175,assembly=GRCh37> 129##contig=<ID=GL000203.1,length=37498,assembly=GRCh37> 130##contig=<ID=GL000246.1,length=38154,assembly=GRCh37> 131##contig=<ID=GL000249.1,length=38502,assembly=GRCh37> 132##contig=<ID=GL000196.1,length=38914,assembly=GRCh37> 133##contig=<ID=GL000248.1,length=39786,assembly=GRCh37> 134##contig=<ID=GL000244.1,length=39929,assembly=GRCh37> 135##contig=<ID=GL000238.1,length=39939,assembly=GRCh37> 136##contig=<ID=GL000202.1,length=40103,assembly=GRCh37> 137##contig=<ID=GL000234.1,length=40531,assembly=GRCh37> 138##contig=<ID=GL000232.1,length=40652,assembly=GRCh37> 139##contig=<ID=GL000206.1,length=41001,assembly=GRCh37> 140##contig=<ID=GL000240.1,length=41933,assembly=GRCh37> 141##contig=<ID=GL000236.1,length=41934,assembly=GRCh37> 142##contig=<ID=GL000241.1,length=42152,assembly=GRCh37> 143##contig=<ID=GL000243.1,length=43341,assembly=GRCh37> 144##contig=<ID=GL000242.1,length=43523,assembly=GRCh37> 145##contig=<ID=GL000230.1,length=43691,assembly=GRCh37> 146##contig=<ID=GL000237.1,length=45867,assembly=GRCh37> 147##contig=<ID=GL000233.1,length=45941,assembly=GRCh37> 148##contig=<ID=GL000204.1,length=81310,assembly=GRCh37> 149##contig=<ID=GL000198.1,length=90085,assembly=GRCh37> 150##contig=<ID=GL000208.1,length=92689,assembly=GRCh37> 151##contig=<ID=GL000191.1,length=106433,assembly=GRCh37> 152##contig=<ID=GL000227.1,length=128374,assembly=GRCh37> 153##contig=<ID=GL000228.1,length=129120,assembly=GRCh37> 154##contig=<ID=GL000214.1,length=137718,assembly=GRCh37> 155##contig=<ID=GL000221.1,length=155397,assembly=GRCh37> 156##contig=<ID=GL000209.1,length=159169,assembly=GRCh37> 157##contig=<ID=GL000218.1,length=161147,assembly=GRCh37> 158##contig=<ID=GL000220.1,length=161802,assembly=GRCh37> 159##contig=<ID=GL000213.1,length=164239,assembly=GRCh37> 160##contig=<ID=GL000211.1,length=166566,assembly=GRCh37> 161##contig=<ID=GL000199.1,length=169874,assembly=GRCh37> 162##contig=<ID=GL000217.1,length=172149,assembly=GRCh37> 163##contig=<ID=GL000216.1,length=172294,assembly=GRCh37> 164##contig=<ID=GL000215.1,length=172545,assembly=GRCh37> 165##contig=<ID=GL000205.1,length=174588,assembly=GRCh37> 166##contig=<ID=GL000219.1,length=179198,assembly=GRCh37> 167##contig=<ID=GL000224.1,length=179693,assembly=GRCh37> 168##contig=<ID=GL000223.1,length=180455,assembly=GRCh37> 169##contig=<ID=GL000195.1,length=182896,assembly=GRCh37> 170##contig=<ID=GL000212.1,length=186858,assembly=GRCh37> 171##contig=<ID=GL000222.1,length=186861,assembly=GRCh37> 172##contig=<ID=GL000200.1,length=187035,assembly=GRCh37> 173##contig=<ID=GL000193.1,length=189789,assembly=GRCh37> 174##contig=<ID=GL000194.1,length=191469,assembly=GRCh37> 175##contig=<ID=GL000225.1,length=211173,assembly=GRCh37> 176##contig=<ID=GL000192.1,length=547496,assembly=GRCh37> 177##contig=<ID=NC_007605,length=171823,assembly=NC_007605.1> 178##expectedGender=Female 179##extendedIlluminaManifestVersion=1.2 180##extendedManifestFile=PsychChip_v1-1_15073391_A1.1.2.extended.csv 181##fileDate=Thu Aug 17 00:44:56 UTC 2017 182##fingerprintGender=Unknown 183##genomeBuild=HG19 184##imagingDate=8/14/2015 7:27:49 PM 185##manifestFile=PsychChip_v1-1_15073391_A1.csv 186##p95Green=7373 187##p95Red=22526 188##picardVersion=1.1222-SNAPSHOT 189##reference=/cromwell_root/broad-references/hg19/v0/Homo_sapiens_assembly19.fasta 190##sampleAlias=NA12878 191##scannerName=N0700 192##source=BPM file 193##zcallThresholds=thresholds.7.txt 194##zcallVersion=1.0.0.0 195#CHROM POS ID REF ALT QUAL FILTER INFO 1961 1007545 . A <NON_REF> 99 . . 1971 1335002 . G <NON_REF> 99 . . 198