Skip to content

Instantly share code, notes, and snippets.

@dwaggott
Created April 28, 2017 18:04
Show Gist options
  • Save dwaggott/3b19cfc9fae0879c970f9f68f258e75f to your computer and use it in GitHub Desktop.
Save dwaggott/3b19cfc9fae0879c970f9f68f258e75f to your computer and use it in GitHub Desktop.
##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>
##contig=<ID=6,length=171115067>
##contig=<ID=7,length=159138663>
##contig=<ID=8,length=146364022>
##contig=<ID=9,length=141213431>
##contig=<ID=10,length=135534747>
##contig=<ID=11,length=135006516>
##contig=<ID=12,length=133851895>
##contig=<ID=13,length=115169878>
##contig=<ID=14,length=107349540>
##contig=<ID=15,length=102531392>
##contig=<ID=16,length=90354753>
##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>
##contig=<ID=GL000229.1,length=19913>
##contig=<ID=GL000231.1,length=27386>
##contig=<ID=GL000210.1,length=27682>
##contig=<ID=GL000239.1,length=33824>
##contig=<ID=GL000235.1,length=34474>
##contig=<ID=GL000201.1,length=36148>
##contig=<ID=GL000247.1,length=36422>
##contig=<ID=GL000245.1,length=36651>
##contig=<ID=GL000197.1,length=37175>
##contig=<ID=GL000203.1,length=37498>
##contig=<ID=GL000246.1,length=38154>
##contig=<ID=GL000249.1,length=38502>
##contig=<ID=GL000196.1,length=38914>
##contig=<ID=GL000248.1,length=39786>
##contig=<ID=GL000244.1,length=39929>
##contig=<ID=GL000238.1,length=39939>
##contig=<ID=GL000202.1,length=40103>
##contig=<ID=GL000234.1,length=40531>
##contig=<ID=GL000232.1,length=40652>
##contig=<ID=GL000206.1,length=41001>
##contig=<ID=GL000240.1,length=41933>
##contig=<ID=GL000236.1,length=41934>
##contig=<ID=GL000241.1,length=42152>
##contig=<ID=GL000243.1,length=43341>
##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>
##contig=<ID=GL000214.1,length=137718>
##contig=<ID=GL000221.1,length=155397>
##contig=<ID=GL000209.1,length=159169>
##contig=<ID=GL000218.1,length=161147>
##contig=<ID=GL000220.1,length=161802>
##contig=<ID=GL000213.1,length=164239>
##contig=<ID=GL000211.1,length=166566>
##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>
##contig=<ID=GL000224.1,length=179693>
##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
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment