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" &&…

I do this similarly for things like the transcript consequences, loftee output, polyphen and sift output, and other things. For reference, here is the schema of the annotations that VEP adds: Edit: it’s not formatting correctly. Let me work on that.

Here’s the script I use: annotatevariants expr -c 'va.transcript_canonicals = va.vep.transcript_consequences.filter(tc => tc.canonical == 1)' \ annotatevariants expr -c 'va.most_severe_csq = let x = va.transcript_canonicals.map(y => y.consequence_terms.toSet) in if (isMissing(x)) va.vep.most_seve…

I love it! This is the way to go. You can simplify as follow: ("H" ~ va.dbNSFP.MutationAssessor_pred || "M" ~ va.dbNSFP.MutationAssessor_pred) as "[HM]" ~ va.dbNSFP.MutationAssessor_pred

I like how detailed yours is. Mine would probably annotate consequence similarly, since it looks for coding consequences, and those are considered more severe than non-coding. I have the potential to pull out multiple terms (like missense_variant and splice_region_variant) together if the transcri…

Parsing VEP output

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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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Parsing VEP output

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