Andrea asked if I could post how I’ve been parsing the VEP output to get things like gene names and transcript consequences. This is what I’ve been doing (within an annotatevariants command): if (isDefined(va.vep.transcript_consequences.find(c => c.canonical == 1 && c.biotype == "protein_coding" &&…

Parsing VEP output

Maryam_Zekavat September 22, 2016, 7:57pm 5

It’s essentially pulling out the most severe, canonical consequence/gene

Accessing fields in structure type

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Transcript_consequences value is missing in matrix table Hail Query & hailctl	21	691	June 30, 2021
Error during VEP annotation (gene_symbol field) of BioBank data Hail Query & hailctl	0	290	July 11, 2023
FYI: VEP annotation inconsistencies gnomad.utils Science	0	676	April 28, 2020