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##fileformat=VCFv4.1
##fileDate=20120730
##center=Complete Genomics
##source=CGAPipeline_2.0.0.26;cgatools_1.6.0
##source_GENOME_REFERENCE=NCBI build 37
##phasing=partial
##ALT=<ID=CGA_NOCALL,Description="No-called record">
##ALT=<ID=CGA_CNVWIN,Description="Copy number analysis window">
##ALT=<ID=INS:ME:ALU,Description="Insertion of ALU element">
##ALT=<ID=INS:ME:L1,Description="Insertion of L1 element">
##ALT=<ID=INS:ME:SVA,Description="Insertion of SVA element">
##ALT=<ID=INS:ME:MER,Description="Insertion of MER element">
##ALT=<ID=INS:ME:LTR,Description="Insertion of LTR element">
##ALT=<ID=INS:ME:PolyA,Description="Insertion of PolyA element">
##ALT=<ID=INS:ME:HERV,Description="Insertion of HERV element">
##FILTER=<ID=VQLOW,Description="Quality not VQHIGH">
##FILTER=<ID=SQLOW,Description="Somatic quality not SQHIGH">
##FILTER=<ID=URR,Description="Too close to an underrepresented repeat">
##FILTER=<ID=MPCBT,Description="Mate pair count below 10">
##FILTER=<ID=SHORT,Description="Junction side length below 70">
##FILTER=<ID=TSNR,Description="Transition sequence not resolved">
##FILTER=<ID=INTERBL,Description="Interchromosomal junction in baseline">
##FILTER=<ID=sns75,Description="Sensitivity to known MEI calls in range (.75,.95] i.e. medium FDR">
##FILTER=<ID=sns95,Description="Sensitivity to known MEI calls in range (.95,1.00] i.e. high to very high FDR">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##source_20130711.1=vcf-merge(r840) --collapse any --remove-duplicates --trim-ALTs --regions 1 /wsu/home/eq/eq83/eq8302/cg_panel/ceph/vcfBeta-NA12877.vcf.gz /wsu/home/eq/eq83/eq8302/cg_panel/ceph/vcfBeta-NA12878.vcf.gz /wsu/home/eq/eq83/eq8302/cg_panel/ceph/vcfBeta-NA12879.vcf.gz /wsu/home/eq/eq83/eq8302/cg_panel/ceph/vcfBeta-NA12880.vcf.gz /wsu/home/eq/eq83/eq8302/cg_panel/ceph/vcfBeta-NA12881.vcf.gz /wsu/home/eq/eq83/eq8302/cg_panel/ceph/vcfBeta-NA12882.vcf.gz /wsu/home/eq/eq83/eq8302/cg_panel/ceph/vcfBeta-NA12883.vcf.gz /wsu/home/eq/eq83/eq8302/cg_panel/ceph/vcfBeta-NA12884.vcf.gz /wsu/home/eq/eq83/eq8302/cg_panel/ceph/vcfBeta-NA12885.vcf.gz /wsu/home/eq/eq83/eq8302/cg_panel/ceph/vcfBeta-NA12886.vcf.gz /wsu/home/eq/eq83/eq8302/cg_panel/ceph/vcfBeta-NA12887.vcf.gz /wsu/home/eq/eq83/eq8302/cg_panel/ceph/vcfBeta-NA12888.vcf.gz /wsu/home/eq/eq83/eq8302/cg_panel/ceph/vcfBeta-NA12889.vcf.gz /wsu/home/eq/eq83/eq8302/cg_panel/ceph/vcfBeta-NA12890.vcf.gz /wsu/home/eq/eq83/eq8302/cg_panel/ceph/vcfBeta-NA12891.vcf.gz /wsu/home/eq/eq83/eq8302/cg_panel/ceph/vcfBeta-NA12892.vcf.gz /wsu/home/eq/eq83/eq8302/cg_panel/ceph/vcfBeta-NA12893.vcf.gz
##sourceFiles_20130711.1=0:/wsu/home/eq/eq83/eq8302/cg_panel/ceph/vcfBeta-NA12877.vcf.gz,1:/wsu/home/eq/eq83/eq8302/cg_panel/ceph/vcfBeta-NA12878.vcf.gz,2:/wsu/home/eq/eq83/eq8302/cg_panel/ceph/vcfBeta-NA12879.vcf.gz,3:/wsu/home/eq/eq83/eq8302/cg_panel/ceph/vcfBeta-NA12880.vcf.gz,4:/wsu/home/eq/eq83/eq8302/cg_panel/ceph/vcfBeta-NA12881.vcf.gz,5:/wsu/home/eq/eq83/eq8302/cg_panel/ceph/vcfBeta-NA12882.vcf.gz,6:/wsu/home/eq/eq83/eq8302/cg_panel/ceph/vcfBeta-NA12883.vcf.gz,7:/wsu/home/eq/eq83/eq8302/cg_panel/ceph/vcfBeta-NA12884.vcf.gz,8:/wsu/home/eq/eq83/eq8302/cg_panel/ceph/vcfBeta-NA12885.vcf.gz,9:/wsu/home/eq/eq83/eq8302/cg_panel/ceph/vcfBeta-NA12886.vcf.gz,10:/wsu/home/eq/eq83/eq8302/cg_panel/ceph/vcfBeta-NA12887.vcf.gz,11:/wsu/home/eq/eq83/eq8302/cg_panel/ceph/vcfBeta-NA12888.vcf.gz,12:/wsu/home/eq/eq83/eq8302/cg_panel/ceph/vcfBeta-NA12889.vcf.gz,13:/wsu/home/eq/eq83/eq8302/cg_panel/ceph/vcfBeta-NA12890.vcf.gz,14:/wsu/home/eq/eq83/eq8302/cg_panel/ceph/vcfBeta-NA12891.vcf.gz,15:/wsu/home/eq/eq83/eq8302/cg_panel/ceph/vcfBeta-NA12892.vcf.gz,16:/wsu/home/eq/eq83/eq8302/cg_panel/ceph/vcfBeta-NA12893.vcf.gz
##INFO=<ID=SF,Number=.,Type=String,Description="Source File (index to sourceFiles, f when filtered)">
##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##SnpEffVersion="3.3h (build 2013-08-11), by Pablo Cingolani"
##SnpEffCmd="SnpEff -lof -motif -hgvs -nextProt GRCh37.71 protocols/ex1.vcf "
##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon | GenotypeNum [ | ERRORS | WARNINGS ] )' ">
##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected' ">
##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected' ">
##SnpSiftVersion="SnpSift 3.3h (build 2013-08-11), by Pablo Cingolani"
##SnpSiftCmd="SnpSift casecontrol -tfam protocols/pedigree.tfam protocols/ex1.eff.vcf "
##INFO=<ID=Cases,Number=3,Type=Integer,Description="Number of variants in cases: Hom, Het, Count">
##INFO=<ID=Controls,Number=3,Type=Integer,Description="Number of variants in controls: Hom, Het, Count">
##INFO=<ID=CC_DOM,Number=1,Type=Float,Description="p-value using dominant model (Fisher exact)">
##INFO=<ID=CC_REC,Number=1,Type=Float,Description="p-value using recessive model (Fisher exact)">
##INFO=<ID=CC_ALL,Number=1,Type=Float,Description="p-value using allele count model (Fisher exact)">
##INFO=<ID=CC_GENO,Number=1,Type=Float,Description="p-value using genotype / codominant model (CochranArmitage)">
##SnpSiftVersion="SnpSift 4.0e (build 2014-09-13), by Pablo Cingolani"
##SnpSiftCmd="SnpSift filter '(Cases[0] = 3) & (Controls[0] = 0)'"
##FILTER=<ID=SnpSift,Description="SnpSift 4.0e (build 2014-09-13), by Pablo Cingolani, Expression used: (Cases[0] = 3) & (Controls[0] = 0)">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12877 NA12878 NA12879 NA12880 NA12881 NA12882 NA12883 NA12884 NA12885 NA12886 NA12887 NA12888 NA12889 NA12890 NA12891 NA12892 NA12893
7 28831958 . G A . . Cases=3,0,6;Controls=0,10,10 GT 1|0 1/0 1/1 . . 1|0 1|0 . 1/1 1/1 1/0 1/0 . 1|0 1/0 1/0 1/0
|
