For example, if I have a list of variants like this:
Gene_ID Transcript Coding Amino_Acid_Change
TP53 NM_000546 c.G830T p.C277F
TP53 NM_001126112 c.G830T p.C277F
TP53 NM_001126113 c.G830T p.C277F
TP53 NM_001126114 c.G830T p.C277F
TP53 NM_001126115 c.G434T p.C145F
TP53 NM_001126116 c.G434T p.C145F
TP53 NM_001126117 c.G434T p.C145F
TP53 NM_001126118 c.G713T p.C238F
How could you figure out which of the transcripts is the canonical transcript?
Supposedly, transcripts are listed in places like UCSC, RefSeq, and Ensembl. But I have gone through each of these and have not been able to find anything that resembles the information I've listed above (ANNOVAR RefGene annotation output). The closest I've come is the UCSC Table Browser returning 'knownCanonical' for UCSC genes, but this is in a BED-style output with identifiers that do not resemble my given data. ANNOVAR's own documentation says that it does not support any differential reporting for canonical transcripts.
2 answers
I presume canonical information can be downloaded from here http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/knownCanonical.txt.gz . But I have not used it. For the species I use lacking such information, I usually determine the longest protein and use it as canonical.
I don't know why biomart does not provide that kind of important information.
Also sorry i accidentally added it as an answer when I meant a comment.
This thread uses table browser to get related ids for all canonical transcripts. http://redmine.soe.ucsc.edu/forum/index.php?t=tree&th=7602&mid=19939&S=f6391396b0b0a7bcd539e058e8edc96b&rev=&reveal=
However it looks like the script I wrote to implement the the cross-referencing described there is still listed here. The gist of it is to match the ID's in knownCanonical.txt against the ones in kgXref.txt. I believe there is also a saved copy of the output in the GitHub repo at that script location as well.
Those are RefSeq IDs, so you are looking for RefSeq info. There is a whole discussion about it here: https://groups.google.com/a/soe.ucsc.edu/forum/#!topic/genome/_6asF5KciPc
If you want to know what is really the "canonical" transcript, that's a whole different story. Canonical is not always canonical.
Update (8/2019): There have been some additional more helpful discussions:
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