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

Topic		Replies	Views
FYI: VEP annotation inconsistencies gnomad.utils Science	0	681	April 28, 2020
Transcript_consequences value is missing in matrix table Hail Query & hailctl	21	696	June 30, 2021
Accessing fields in structure type Help [0.1]	3	1170	October 12, 2017
VEP fails to generate annotations Help [0.1]	17	2162	June 19, 2018
VEP: add field hgvsg Hail Query & hailctl	2	677	November 18, 2019