VCF specification question

geertvandeweyer · 08-25-2016, 02:04 AM

Hi,

I couldn't find this in the VCF specification documents. Is it allowed to have two lines in a VCF with the same variant, identical format & sample columns but different info fields?

edit: added example (eg. ExAC.Info.AF is different between the two lines):

Quote:

22 42523528 rs1058172 C T . PASS DP=3797;AF=0.074;CB=UM,BI,BC;EUR_R2=0.823;AFR_R2=0.825;dbNSFP.FathmmPred=D|D|D;dbNSFP.FathmmRankscore=0.97505;dbNSFP.FathmmScore=-4.41|-4.41|-4.41;dbNSFP.Gerp++Nr=4.93;dbNSFP.Gerp++Rs=4.93;dbNSFP.Gerp++RsRankscore=0.64822;dbNSFP.LrtPred=D;dbNSFP.LrtScore=0.000001;dbNSFP.MutationassessorPred=H;dbNSFP.MutationassessorRankscore=0.99545;dbNSFP.MutationassessorScore=4.62;dbNSFP.MutationtasterConvertedRankscore=0.70825;dbNSFP.MutationtasterPred=P;dbNSFP.MutationtasterScore=0.000;dbNSFP.Phastcons46wayPrimate=0.957000;dbNSFP.Phastcons46wayPrimateRankscore=0.61999;dbNSFP.Phylop46wayPrimate=0.555000;dbNSFP.Phylop46wayPrimateRankscore=0.69702;dbNSFP.Polyphen2HdivPred=D|D|D;dbNSFP.Polyphen2HdivRankscore=0.89917;dbNSFP.Polyphen2HdivScore=1.0|0.999|1.0;dbNSFP.Polyphen2HvarPred=D|D|D;dbNSFP.Polyphen2HvarRankscore=0.91635;dbNSFP.Polyphen2HvarScore=0.999|0.978|0.999;dbNSFP.Pos=42523528;dbNSFP.RadialsvmPred=T;dbNSFP.RadialsvmRankscore=0.49943;dbNSFP.RadialsvmScore=-0.8885;dbNSFP.SiftConvertedRankscore=0.87932;dbNSFP.SiftPred=D;dbNSFP.SiftScore=0;dbNSFP.Siphy29wayLogodds=17.7329;dbNSFP.Siphy29wayLogoddsRankscore=0.88383;dbNSFP.Vest3Rankscore=0.93136;dbNSFP.Vest3Score=0.937;ExAC.Info.AC=15149;ExAC.Info.AN=126630;ExAC.Info.AF=0.120;ExAC.Info.AC_Het=14922;ExAC.Info.AC_Hom=11;Effect_Impact=MODIFIER;Gene_Name=NDUFA6-AS1;Transcript_BioType=antisense;Gene_Coding=NON_CODING;Transcript_ID=ENST00000416037;Exon_Rank=5;Genotype_Number=1;TYPE=SNP;ENST=ENST00000360608;GENE=CYP2D6;INFO=-/4.4kb/9/1.7kb;LOC=Ex7;HGVS=c.1094G>A_p.Arg365His;SAVANT_EFFECT=NONSYNONYMOUS;SAVANT_IMPACT=MODERATE;CLASS=NSC;ALTANN=None GT:AD

P:GD:GL:GQ:OG 0|1:.:.:.:.:5.07:./.
22 42523528 rs1058172 C T . PASS DP=3797;AF=0.074;CB=UM,BI,BC;EUR_R2=0.823;AFR_R2=0.825;dbNSFP.FathmmPred=D|D|D;dbNSFP.FathmmRankscore=0.97505;dbNSFP.FathmmScore=-4.41|-4.41|-4.41;dbNSFP.Gerp++Nr=4.93;dbNSFP.Gerp++Rs=4.93;dbNSFP.Gerp++RsRankscore=0.64822;dbNSFP.LrtPred=D;dbNSFP.LrtScore=0.000001;dbNSFP.MutationassessorPred=H;dbNSFP.MutationassessorRankscore=0.99545;dbNSFP.MutationassessorScore=4.62;dbNSFP.MutationtasterConvertedRankscore=0.70825;dbNSFP.MutationtasterPred=P;dbNSFP.MutationtasterScore=0.000;dbNSFP.Phastcons46wayPrimate=0.957000;dbNSFP.Phastcons46wayPrimateRankscore=0.61999;dbNSFP.Phylop46wayPrimate=0.555000;dbNSFP.Phylop46wayPrimateRankscore=0.69702;dbNSFP.Polyphen2HdivPred=D|D|D;dbNSFP.Polyphen2HdivRankscore=0.89917;dbNSFP.Polyphen2HdivScore=1.0|0.999|1.0;dbNSFP.Polyphen2HvarPred=D|D|D;dbNSFP.Polyphen2HvarRankscore=0.91635;dbNSFP.Polyphen2HvarScore=0.999|0.978|0.999;dbNSFP.Pos=42523528;dbNSFP.RadialsvmPred=T;dbNSFP.RadialsvmRankscore=0.49943;dbNSFP.RadialsvmScore=-0.8885;dbNSFP.SiftConvertedRankscore=0.87932;dbNSFP.SiftPred=D;dbNSFP.SiftScore=0;dbNSFP.Siphy29wayLogodds=17.7329;dbNSFP.Siphy29wayLogoddsRankscore=0.88383;dbNSFP.Vest3Rankscore=0.93136;dbNSFP.Vest3Score=0.937;ExAC.Info.AC=1;ExAC.Info.AN=126630;ExAC.Info.AF=7.897e-06;ExAC.Info.AC_Het=14922;ExAC.Info.AC_Hom=11;Effect_Impact=MODIFIER;Gene_Name=NDUFA6-AS1;Transcript_BioType=antisense;Gene_Coding=NON_CODING;Transcript_ID=ENST00000416037;Exon_Rank=5;Genotype_Number=1;TYPE=SNP;ENST=ENST00000360608;GENE=CYP2D6;INFO=-/4.4kb/9/1.7kb;LOC=Ex7;HGVS=c.1094G>A_p.Arg365His;SAVANT_EFFECT=NONSYNONYMOUS;SAVANT_IMPACT=MODERATE;CLASS=NSC;ALTANN=None GT:AD

P:GD:GL:GQ:OG 0|1:.:.:.:.:5.07:./.

vivek_ · 08-25-2016, 06:05 AM

How do you get different allele allele frequencies in ExAC for the same alternate allele and location?

geertvandeweyer · 08-25-2016, 06:15 AM

good question. It's not my VCF, so I was wondering the same thing...

vivek_ · 08-25-2016, 06:20 AM

Quote:

Originally Posted by geertvandeweyer

good question. It's not my VCF, so I was wondering the same thing...

Looks like it is a different alternate allele. So the VCF is inaccurate.

http://exac.broadinstitute.org/dbsnp/rs1058172

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08-25-2016, 06:05 AM	#2
vivek_ PhD Student Location: Denmark Join Date: Jul 2012 Posts: 164	How do you get different allele allele frequencies in ExAC for the same alternate allele and location?

08-25-2016, 06:15 AM	#3
geertvandeweyer Member Location: Antwerp, Belgium Join Date: Jan 2011 Posts: 14	good question. It's not my VCF, so I was wondering the same thing...