REQUIRED for all errors and issues:
a) GATK version used: v22.214.171.124
b) Exact command used:
I've been using Funcotator for variant annotation and ran into something confusing. I noticed an issue similar to this one: GATK Funcotator Transcript Selection Criteria, but didn't find a clear answer there.
So, I used Funcotator on my germline sequencing data and found some variants labeled as 'intronic', like MUTYH (ENST00000531105.5). But the canonical transcript for this one actually shows a missense mutation in a protein-coding transcript. Although the "Other Transcripts" column in Funcotator lists these variants, I'm not sure why they aren't the main ones.
I also saw an option on the Funcotator tutorial page to pick between "BEST EFFECT" or "CANONICAL" for the transcript type. But what happens if I don’t provide a list? I get that "CANONICAL" is the default, but then shouldn’t the splice variant be protein-coding and not intronic?
If anyone can clear this up for me, that'd be awesome!
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