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vcf: Handling structured header records with missing IDs in VCF 4.1/4.2 #760

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zaeleus opened this issue Mar 11, 2024 · 0 comments
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zaeleus commented Mar 11, 2024

In VCF 4.3, the concept of structured and unstructured records was introduced, which requires all structured records to include an ID field (§ 1.4 "Meta-information lines" (2022-11-27)). Was this a clarification or a change from previous versions?

VCF 4.1 and 4.2 don't define what header lines are. How are they expected to be parsed? Specifically, I'm interested in how structured header records with missing IDs are supposed to be handled/interpreted.

For example,

$ curl --silent https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/archive_2.0/2017/clinvar_20170516.vcf.gz | gzip -d | head | grep --extended-regexp "^##(fileformat|ID)"
##fileformat=VCFv4.1
##ID=<Description="ClinVar Variation ID">
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