VCF headers describing the content of the INFO field are supposed to give additional information about a variant.

Example. A VCF file can be annotated against genomic variant databases such as dbSNP or ClinVar. The annotations such databases add to the file are described in the headers.

For instance, the CLNSIG field (taken from ClinVar) describes the clinical significance of a variant. Such field description is contained in the following header:

##INFO=<ID=CLNSIG,Number=.,Type=String,Description="Variant Clinical Significance, 0 - Uncertain significance, 1 - not provided, 2 - Benign, 3 - Likely benign, 4 - Likely pathogenic, 5 - Pathogenic, 6 - drug response, 7 - histocompatibility, 255 - other">

As reported in the field definition, the set of values it can take changes over time:

Other non-standard terms are also used to meet submitter needs. ClinVar plans to add standard terms for other scenarios (e.g. somatic, pharmacogenomic, and mitochondrial variants) when they are available.

Do you know if this is a standard condition? Are headers supposed to change a lot over time? Is this condition valid only for clinical annotations (such as the ones provided by ClinVar), or something that is supposed to be considered for every annotation?

Thank you for your help.

  • $\begingroup$ As always with annotations, the annotation of a .vcf-file reflects the current knowledge. If that knowledge changes, the header of a file can be updated. Usually, this is not something you do by yourself but the providers of the file release new versions. However, I have no experience with clinical data and my statement is purely based on personal experience and common sense. $\endgroup$ – AlexDeLarge Apr 4 '17 at 7:56

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