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April 28, 2017 18:04
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##fileformat=VCFv4.2 | |
##FILTER=<ID=PASS,Description="All filters passed"> | |
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | |
##FILTER=<ID=RF,Description="Failed random forests filters (SNV cutoff 0.1, indels cutoff 0.2)"> | |
##FILTER=<ID=AC0,Description="Allele Count is zero (i.e. no high-confidence genotype (GQ >= 20, DP >= 10, AB => 0.2 for het calls))"> | |
##FILTER=<ID=InbreedingCoeff,Description="InbreedingCoeff < -0.3"> | |
##FILTER=<ID=LCR,Description="In a low complexity region"> | |
##FILTER=<ID=SEGDUP,Description="In a segmental duplication region"> | |
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency among genotypes, for each ALT allele, in the same order as listed"> | |
##INFO=<ID=AF_POPMAX,Number=A,Type=Float,Description="Maximum Allele Frequency across populations (excluding OTH)"> | |
##contig=<ID=1,length=249250621> | |
##contig=<ID=2,length=243199373> | |
##contig=<ID=3,length=198022430> | |
##contig=<ID=4,length=191154276> | |
##contig=<ID=5,length=180915260> | |
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##contig=<ID=7,length=159138663> | |
##contig=<ID=8,length=146364022> | |
##contig=<ID=9,length=141213431> | |
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##contig=<ID=11,length=135006516> | |
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##contig=<ID=17,length=81195210> | |
##contig=<ID=18,length=78077248> | |
##contig=<ID=19,length=59128983> | |
##contig=<ID=20,length=63025520> | |
##contig=<ID=21,length=48129895> | |
##contig=<ID=22,length=51304566> | |
##contig=<ID=X,length=155270560> | |
##contig=<ID=Y,length=59373566> | |
##contig=<ID=MT,length=16569> | |
##contig=<ID=GL000207.1,length=4262> | |
##contig=<ID=GL000226.1,length=15008> | |
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##contig=<ID=GL000231.1,length=27386> | |
##contig=<ID=GL000210.1,length=27682> | |
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##contig=<ID=GL000242.1,length=43523> | |
##contig=<ID=GL000230.1,length=43691> | |
##contig=<ID=GL000237.1,length=45867> | |
##contig=<ID=GL000233.1,length=45941> | |
##contig=<ID=GL000204.1,length=81310> | |
##contig=<ID=GL000198.1,length=90085> | |
##contig=<ID=GL000208.1,length=92689> | |
##contig=<ID=GL000191.1,length=106433> | |
##contig=<ID=GL000227.1,length=128374> | |
##contig=<ID=GL000228.1,length=129120> | |
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##contig=<ID=GL000218.1,length=161147> | |
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##contig=<ID=GL000199.1,length=169874> | |
##contig=<ID=GL000217.1,length=172149> | |
##contig=<ID=GL000216.1,length=172294> | |
##contig=<ID=GL000215.1,length=172545> | |
##contig=<ID=GL000205.1,length=174588> | |
##contig=<ID=GL000219.1,length=179198> | |
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##contig=<ID=GL000223.1,length=180455> | |
##contig=<ID=GL000195.1,length=182896> | |
##contig=<ID=GL000212.1,length=186858> | |
##contig=<ID=GL000222.1,length=186861> | |
##contig=<ID=GL000200.1,length=187035> | |
##contig=<ID=GL000193.1,length=189789> | |
##contig=<ID=GL000194.1,length=191469> | |
##contig=<ID=GL000225.1,length=211173> | |
##contig=<ID=GL000192.1,length=547496> | |
##contig=<ID=NC_007605,length=171823> | |
##reference=file:///seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta | |
##bcftools_normVersion=1.4-1-g55dc0fe+htslib-1.3.2-252-g5c695a1 | |
##bcftools_normCommand=norm -f /share/PI/euan/apps/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -m- gnomad.exomes.r2.0.1.sites.vcf.gz; Date=Thu Apr 13 09:51:38 2017 | |
##bcftools_annotateVersion=1.4-1-g55dc0fe+htslib-1.3.2-252-g5c695a1 | |
##bcftools_annotateCommand=annotate -x FORMAT,^INFO/AF,INFO/AF_POPMAX -O z; Date=Thu Apr 13 09:51:38 2017 | |
##bcftools_viewVersion=1.4-1-g55dc0fe+htslib-1.3.2-252-g5c695a1 | |
##bcftools_viewCommand=view -i AF_POPMAX<0.01 -O z gnomad.exomes.r2.0.1.sites.slim.vcf.gz; Date=Thu Apr 13 10:17:41 2017 | |
##bcftools_isecVersion=1.4+htslib-1.4 | |
##bcftools_isecCommand=isec -O z -n =2 -w 1 -R candidate_genes.bed.gz /scratch/PI/euan/common/gnomad_data/vcf/exomes/gnomad.exomes.r2.0.1.sites_popmax_lt1pc.vcf.gz /scratch/PI/euan/common/dbsnp/b37/common_all_20170403_norm.vcf.gz; Date=Thu Apr 27 17:13:03 2017 | |
##bcftools_viewVersion=1.4+htslib-1.4 | |
##bcftools_viewCommand=view -O z -r 11:111781158 gnomad_wes_rare_af.vcf.gz; Date=Fri Apr 28 10:55:53 2017 | |
#CHROM POS ID REF ALT QUAL FILTER INFO | |
11 111781158 rs542645787 C G 2079.37 PASS AF=4.06081e-06;AF_POPMAX=6.53424e-05 |
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