fix(workflow): stop scheduling VEP annotation in the pipeline - #840
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bencap merged 1 commit intoAug 12, 2026
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VEP consequences were sourced from the top-level most_severe_consequence, which reports the worst call across all overlapping transcripts instead of the transcript the variant was actually mapped to, producing misleading annotations. The job definition is left commented out rather than deleted so it can be restored once VEP annotates Allele rows directly. Refs #772
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VEP consequences were sourced from the top-level most_severe_consequence, which reports the worst call across all overlapping transcripts instead of the transcript the variant was actually mapped to, producing misleading annotations.
The job definition is left commented out rather than deleted so it can be restored once VEP annotates Allele rows directly.
See #772