We used Funcotator to annotate somatic calls and were confused about the transcript selection mode, the default "canonical" mode sometimes chooses a different transcript than what is better known in clinical settings.
1. If we use the transcript-selection-list (e.g. transcriptList.exact_uniprot_matches.AKT1_CRLF2_FGFR1.txt from public gatk bucket), the BRAF hotspot will be annotated with V640E instead of V600E.
2. With canonical mode, EGFR_ELREA701del|L813R is chosen instead of the more commonly known ELREA746del + L858R.
1) how "canonical" is defined for protein change annotation by default?
2) how is the reference file (transcriptList.exact_uniprot_matches.AKT1_CRLF2_FGFR1.txt) made, and what problem does it address?
Thanks a lot.
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