VCF versioning, changelogs, documentation

[davmlaw]

Q1. Could you please clarify a recent change to the VCF file?

There was a recent (as far as I can tell) undocumented change to the VCF format - it appears that recently the INFO field CLNREVSTAT" - ClinVar's review status of the germline classfication for the Variation ID had some new values appear:

• no_classification_provided
• no_classification_for_the_single_variant
• criteria_provided,_conflicting_classifications

Are these new or replacements for the old one?

• no_interpretation_for_the_single_variant -> no_classification_for_the_single_variant
• criteria_provided,_conflicting_interpretations -> criteria_provided,_conflicting_classifications

Q2. Can you please document review statuses on the webpage using consistent terms

This page https://www.ncbi.nlm.nih.gov/clinvar/docs/review_status/ seems to review statuses that don't match the old or new VCF format: eg "no assertion for the individual variant" - is this a 3rd representation of the same status ("no_interpretation_for_the_single_variant" and "no_classification_for_the_single_variant")?

Another possibility is to have a CHANGELOG on the GitHub to document the VCF

Q3. ClinVar VCF format version

Could you please consider introducing a "ClinVar VCF version" (semantic versions) that is in the VCF header?

That way VCF consumers can know whether there are breaking changes to the format