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example.vcf.txt
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example.vcf.txt
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##fileformat=VCFv4.2
##fileurl=https://github.com/MRCIEU/gwas-vcf-specification/blob/master/example.vcf.txt
##filedate="07/09/2020"
##gwasformat=GWAS-VCFv1.2
##source=Gwas2VCFv1.2.0
##reference=ftp://ftp.broadinstitute.org/bundle/b37/human_g1k_v37.fasta.gz
##contig=<ID=1,length=249250621,assembly=GRCh37.p13>
##contig=<ID=2,length=243199373,assembly=GRCh37.p13>
##contig=<ID=3,length=198022430,assembly=GRCh37.p13>
##contig=<ID=4,length=191154276,assembly=GRCh37.p13>
##contig=<ID=5,length=180915260,assembly=GRCh37.p13>
##contig=<ID=6,length=171115067,assembly=GRCh37.p13>
##contig=<ID=7,length=159138663,assembly=GRCh37.p13>
##contig=<ID=8,length=146364022,assembly=GRCh37.p13>
##contig=<ID=9,length=141213431,assembly=GRCh37.p13>
##contig=<ID=10,length=135534747,assembly=GRCh37.p13>
##contig=<ID=11,length=135006516,assembly=GRCh37.p13>
##contig=<ID=12,length=133851895,assembly=GRCh37.p13>
##contig=<ID=13,length=115169878,assembly=GRCh37.p13>
##contig=<ID=14,length=107349540,assembly=GRCh37.p13>
##contig=<ID=15,length=102531392,assembly=GRCh37.p13>
##contig=<ID=16,length=90354753,assembly=GRCh37.p13>
##contig=<ID=17,length=81195210,assembly=GRCh37.p13>
##contig=<ID=18,length=78077248,assembly=GRCh37.p13>
##contig=<ID=19,length=59128983,assembly=GRCh37.p13>
##contig=<ID=20,length=63025520,assembly=GRCh37.p13>
##contig=<ID=21,length=48129895,assembly=GRCh37.p13>
##contig=<ID=22,length=51304566,assembly=GRCh37.p13>
##contig=<ID=X,length=155270560,assembly=GRCh37.p13>
##contig=<ID=Y,length=59373566,assembly=GRCh37.p13>
##FILTER=<ID=PASS,Description="All filters passed">
##INFO=<ID=RSID,Number=1,Type=String,Description="dbSNP identifier",Source="https://ftp.ncbi.nih.gov/snp/latest_release/VCF/GCF_000001405.25.gz",Version="153">
##FORMAT=<ID=NS,Number=A,Type=Float,Description="Variant-specific number of samples/individuals with called genotypes used to test association with specified trait">
##FORMAT=<ID=EZ,Number=A,Type=Float,Description="Z-score provided if it was used to derive the ES and SE fields">
##FORMAT=<ID=SI,Number=A,Type=Float,Description="Accuracy score of summary association statistics imputation">
##FORMAT=<ID=NC,Number=A,Type=Float,Description="Variant-specific number of cases used to estimate genetic effect (binary traits only)">
##FORMAT=<ID=ES,Number=A,Type=Float,Description="Effect size estimate relative to the alternative allele">
##FORMAT=<ID=SE,Number=A,Type=Float,Description="Standard error of effect size estimate">
##FORMAT=<ID=LP,Number=A,Type=Float,Description="-log10 p-value for effect estimate">
##FORMAT=<ID=AF,Number=A,Type=Float,Description="Alternative allele frequency in trait subset">
##FORMAT=<ID=AC,Number=A,Type=Float,Description="Alternative allele count in the trait subset">
##study=<ID="12345678",Source="PubMed",Description="Bibliographic citation of main publication",URL="https://pubmed.ncbi.nlm.nih.gov/12345678">
##trait=<ID="EFO0004340",Description="Body mass index",Source="EFO",Version="3.14.0",Type="continuous",Test="linear",Unit="SD",Population="European",TotalSamples=461460,TotalVariants=9851866,VariantsNotRead=0,HarmonisedVariants=9851866,VariantsNotHarmonised=0,SwitchedAlleles=9851866,FileUrl="https://gwas.mrcieu.ac.uk/files/ukb-b-19953/ukb-b-19953.vcf.gz",FileDate="24/04/2020">
##trait=<ID="EFO0001360",Description="type II diabetes mellitus",Source="EFO",Version="3.14.0",Type="binary",Test="logistic",Population="European",TotalSamples=462933,TotalCases=2972,TotalVariants=9851866,VariantsNotRead=0,HarmonisedVariants=9851866,VariantsNotHarmonised=0,SwitchedAlleles=9851866,FileUrl="https://gwas.mrcieu.ac.uk/files/ukb-b-13806/ukb-b-13806.vcf.gz",FileDate="24/04/2020">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT EFO0004340 EFO0001360
1 49298 . T C . PASS RSID=rs10399793 NS:NC:ES:SE:LP:AF:AC 463005:0:0.00103892:0.0034984:0.113509:0.613764:568351 463005:2972:9.098e-05:0.000294716:0.119186:0.613764:568351
1 49298 . T A . PASS RSID=rs10399793 NS:NC:ES:SE:LP:AF:AC 463005:0:0.00214602:0.00346583:0.267606:0.011:4630 463005:2972:0.000102689:0.00029197:0.136677:0.012:4630
1 91536 . GTC G . PASS RSID=rs6702460 NS:NC:ES:SE:LP:AF:AC 463005:0:0.00410514:0.0034125:0.638272:0.456845:423042 463005:2972:0.000329732:0.000287485:0.60206:0.456851:423042
1 534192 . C T . PASS RSID=rs6680723 NS:NC:ES:SE:LP:AF:AC 463005:0:0.000334321:0.0038979:0.0315171:0.24094:223131 463005:2972:0.000106473:0.000328379:0.124939:0.24096:223131
1 706368 . A AAA . PASS RSID=rs12029736 NS:NC:ES:SE:LP:AF:AC 463005:0:-0.00030371:0.00241981:0.0457575:0.515705:477487 463005:2972:7.16085e-06:0.000203854:0.0132283:0.51565:477487