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17 months ago
Arda
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I have downloaded a VCF file from 1000genomes for chromosome 5. It is my understanding that the format field shows which allele a variant occurs 1|0 means it occurs on the left allele 0|0 means it does not occur etc., but in this vcf file some samples show some variants (I have only seen this in structural variants) like 0|2 what does this mean? Below is the copy paste of two example VCF entries
73,0;AFR_AF=0.0204,0.3427,0.0809,0.0696,0.0061;EUR_AF=0.0258,0.1829,0.0706,0.007,0.007;SAS_AF=0.0317,0.1851,0.046,0.0184,0.002;VT=SV;EX_TARGET;ANNOVAR_DATE=2020-06-08;Func.refGene=.;Gene.refGene=.;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;SIFT_score=.;SIF
T_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_pred=
.;VEST3_score=.;CADD_raw=.;CADD_phred=.;DANN_score=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_pred=.;MetaSVM_score=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_pred=.;integrated_fitCons_score=.;integrated_confidence_value=.;GERP++_RS=.;phyloP7way_vertebrate=.;phyloP20way_mamma
lian=.;phastCons7way_vertebrate=.;phastCons20way_mammalian=.;SiPhy_29way_logOdds=.;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;ALLELE_END;ANNOVAR_DATE=2020-06-08;Func.refGene=.;Gene.refGene=.;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;SIFT_score=.;SI
FT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_pred
=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;DANN_score=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_pred=.;MetaSVM_score=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_pred=.;integrated_fitCons_score=.;integrated_confidence_value=.;GERP++_RS=.;phyloP7way_vertebrate=.;phyloP20way_mamm
alian=.;phastCons7way_vertebrate=.;phastCons20way_mammalian=.;SiPhy_29way_logOdds=.;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;ALLELE_END;ANNOVAR_DATE=2020-06-08;Func.refGene=.;Gene.refGene=.;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;SIFT_score=.;S
IFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_pre
d=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;DANN_score=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_pred=.;MetaSVM_score=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_pred=.;integrated_fitCons_score=.;integrated_confidence_value=.;GERP++_RS=.;phyloP7way_vertebrate=.;phyloP20way_mam
malian=.;phastCons7way_vertebrate=.;phastCons20way_mammalian=.;SiPhy_29way_logOdds=.;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;ALLELE_END;ANNOVAR_DATE=2020-06-08;Func.refGene=.;Gene.refGene=.;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;SIFT_score=.;
SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_pr
ed=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;DANN_score=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_pred=.;MetaSVM_score=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_pred=.;integrated_fitCons_score=.;integrated_confidence_value=.;GERP++_RS=.;phyloP7way_vertebrate=.;phyloP20way_ma
mmalian=.;phastCons7way_vertebrate=.;phastCons20way_mammalian=.;SiPhy_29way_logOdds=.;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;ALLELE_END;ANNOVAR_DATE=2020-06-08;Func.refGene=.;Gene.refGene=.;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;SIFT_score=.
;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_p
red=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;DANN_score=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_pred=.;MetaSVM_score=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_pred=.;integrated_fitCons_score=.;integrated_confidence_value=.;GERP++_RS=.;phyloP7way_vertebrate=.;phyloP20way_m
ammalian=.;phastCons7way_vertebrate=.;phastCons20way_mammalian=.;SiPhy_29way_logOdds=.;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;ALLELE_END GT 0|0 1|0 0|0 0|0 0|2
5 788137 . T <CN0>,<CN2>,<CN3>,<CN4>,<CN5> 100 PASS AC=1,1,0,0,0;AF=0.0279553,0.184105,0.0303514,0.00798722,0.000998403;AN=10;CS=DUP_gs;END=797761;NS=2504;SVTYPE=CNV;DP=44404;EAS_AF=0.0149,0.1637,0.0704,0.0208,0.001;AMR_AF=0.0274,0.1196,0.0115,0.
0014,0.0014;AFR_AF=0.0318,0.3177,0.0363,0.0121,0.0015;EUR_AF=0.0338,0.1382,0.005,0.001,0.001;SAS_AF=0.0307,0.1176,0.0204,0.001,0;VT=SV;ANNOVAR_DATE=2020-06-08;Func.refGene=.;Gene.refGene=.;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;SIFT_score=.;SIFT_pred=.
;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_pred=.;VEST3_
score=.;CADD_raw=.;CADD_phred=.;DANN_score=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_pred=.;MetaSVM_score=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_pred=.;integrated_fitCons_score=.;integrated_confidence_value=.;GERP++_RS=.;phyloP7way_vertebrate=.;phyloP20way_mammalian=.;p
hastCons7way_vertebrate=.;phastCons20way_mammalian=.;SiPhy_29way_logOdds=.;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;ALLELE_END;ANNOVAR_DATE=2020-06-08;Func.refGene=.;Gene.refGene=.;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;SIFT_score=.;SIFT_pred=
.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_pred=.;VEST3
_score=.;CADD_raw=.;CADD_phred=.;DANN_score=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_pred=.;MetaSVM_score=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_pred=.;integrated_fitCons_score=.;integrated_confidence_value=.;GERP++_RS=.;phyloP7way_vertebrate=.;phyloP20way_mammalian=.;
phastCons7way_vertebrate=.;phastCons20way_mammalian=.;SiPhy_29way_logOdds=.;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;ALLELE_END;ANNOVAR_DATE=2020-06-08;Func.refGene=.;Gene.refGene=.;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;SIFT_score=.;SIFT_pred
=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_pred=.;VEST
3_score=.;CADD_raw=.;CADD_phred=.;DANN_score=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_pred=.;MetaSVM_score=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_pred=.;integrated_fitCons_score=.;integrated_confidence_value=.;GERP++_RS=.;phyloP7way_vertebrate=.;phyloP20way_mammalian=.
;phastCons7way_vertebrate=.;phastCons20way_mammalian=.;SiPhy_29way_logOdds=.;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;ALLELE_END;ANNOVAR_DATE=2020-06-08;Func.refGene=.;Gene.refGene=.;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;SIFT_score=.;SIFT_pre
d=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_pred=.;VES
T3_score=.;CADD_raw=.;CADD_phred=.;DANN_score=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_pred=.;MetaSVM_score=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_pred=.;integrated_fitCons_score=.;integrated_confidence_value=.;GERP++_RS=.;phyloP7way_vertebrate=.;phyloP20way_mammalian=
.;phastCons7way_vertebrate=.;phastCons20way_mammalian=.;SiPhy_29way_logOdds=.;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;ALLELE_END;ANNOVAR_DATE=2020-06-08;Func.refGene=.;Gene.refGene=.;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;SIFT_score=.;SIFT_pr
ed=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_pred=.;VE
ST3_score=.;CADD_raw=.;CADD_phred=.;DANN_score=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_pred=.;MetaSVM_score=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_pred=.;integrated_fitCons_score=.;integrated_confidence_value=.;GERP++_RS=.;phyloP7way_vertebrate=.;phyloP20way_mammalian
=.;phastCons7way_vertebrate=.;phastCons20way_mammalian=.;SiPhy_29way_logOdds=.;CLINSIG=.;CLNDBN=.;CLNACC=.;CLNDSDB=.;CLNDSDBID=.;ALLELE_END GT 0|0 1|0 0|0 0|0 0|2
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