Question: Pipes within VCF INFO Column
0
gravatar for basay3
11 weeks ago by
basay30
basay30 wrote:

Sorry if this has been posted before but I cannot find an answer anywhere. I am trying to make sense of the INFO column of a .vcf file that was generated using whole exome sequencing (Illumina). Specifically, what do the number of pipes mean in the data below (| vs || vs ||||, etc.). Thanks!

ANN=A|intron_variant|MODIFIER|PSAP|5660|Transcript|NM_001042465.1|protein_coding||13/14|NM_001042465.1:c.1441-22C>T|||||||rs885828||-1||SNV|EntrezGene||YES||||NP_001035930.1|||||G|G||||||||10:g.73578503G>A|0.4062|0.4592|0.3689|0.5982|0.2793|0.2935|0.4392|0.2714|0.3389|0.4469|0.4446|0.2387|0.6208|0.3522|0.2768|0.3038|0.2545|0.6208|gnomAD_EAS|benign|||18639233||||,A|intron_variant|MODIFIER|PSAP|5660|Transcript|NM_001042465.2|protein_coding||13/14|NM_001042465.2:c.1441-22C>T|||||||rs885828||-1||SNV|EntrezGene||YES||||NP_001035930.1|||||G|G|OK|||||||10:g.73578503G>A|0.4062|0.4592|0.3689|0.5982|0.2793|0.2935|0.4392|0.2714|0.3389|0.4469|0.4446|0.2387|0.6208|0.3522|0.2768|0.3038|0.2545|0.6208|gnomAD_EAS|benign|||18639233||||,A|intron_variant|MODIFIER|PSAP|5660|Transcript|NM_001042466.1|protein_coding||13/14|NM_001042466.1:c.1438-22C>T|||||||rs885828||-1||SNV|EntrezGene||||||NP_001035931.1|||||G|G||||||||10:g.73578503G>A|0.4062|0.4592|0.3689|0.5982|0.2793|0.2935|0.4392|0.2714|0.3389|0.4469|0.4446|0.2387|0.6208|0.3522|0.2768|0.3038|0.2545|0.6208|gnomAD_EAS|benign|||18639233||||,A|intron_variant|MODIFIER|PSAP|5660|Transcript|NM_001042466.2|protein_coding||13/14|NM_001042466.2:c.1438-22C>T|||||||rs885828||-1||SNV|EntrezGene||||||NP_001035931.1|||||G|G|OK|||||||10:g.73578503G>A|0.4062|0.4592|0.3689|0.5982|0.2793|0.2935|0.4392|0.2714|0.3389|0.4469|0.4446|0.2387|0.6208|0.3522|0.2768|0.3038|0.2545|0.6208|gnomAD_EAS|benign|||18639233||||,A|intron_variant|MODIFIER|PSAP|5660|Transcript|NM_002778.2|protein_coding||12/13|NM_002778.2:c.1432-22C>T|||||||rs885828||-1||SNV|EntrezGene||||||NP_002769.1|||||G|G||||||||10:g.73578503G>A|0.4062|0.4592|0.3689|0.5982|0.2793|0.2935|0.4392|0.2714|0.3389|0.4469|0.4446|0.2387|0.6208|0.3522|0.2768|0.3038|0.2545|0.6208|gnomAD_EAS|benign|||18639233||||,A|intron_variant|MODIFIER|PSAP|5660|Transcript|NM_002778.3|protein_coding||12/13|NM_002778.3:c.1432-22C>T|||||||rs885828||-1||SNV|EntrezGene||||||NP_002769.1|||||G|G|OK|||||||10:g.73578503G>A|0.4062|0.4592|0.3689|0.5982|0.2793|0.2935|0.4392|0.2714|0.3389|0.4469|0.4446|0.2387|0.6208|0.3522|0.2768|0.3038|0.2545|0.6208|gnomAD_EAS|benign|||18639233||||
ADD COMMENTlink modified 11 weeks ago by genomax84k • written 11 weeks ago by basay30
0
gravatar for Pierre Lindenbaum
11 weeks ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum128k wrote:

pipe '|' is just a separator '||' means that there is a missing value.

You should have a look at the ANN spec for snpEff: http://snpeff.sourceforge.net/VCFannotationformat_v1.0.pdf

ADD COMMENTlink written 11 weeks ago by Pierre Lindenbaum128k

Thanks for the answer and the link! The vcf file makes much more sense after reading that documentation you provided.

ADD REPLYlink written 11 weeks ago by basay30

it it answers you need, please validate+close by clicking the green mark on the left

ADD REPLYlink written 11 weeks ago by Pierre Lindenbaum128k
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