Pipes within VCF INFO Column

Question

[basay3]

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||||

Answer 1

[Pierre Lindenbaum]

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

[basay3]

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

[Pierre Lindenbaum]

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