Entering edit mode
3.6 years ago
hkarakurt
▴
190
Hello everyone, I have a small list of variants and I want to annotate them with myvariant.info API with a friend. It looks okay but in a variant (http://myvariant.info/v1/variant/chrX:g.153296529G>T) we noticed multiple entries of "HGVS Coding" section. As I know, these are the possible transcripts and one of them is the canonical transcript. I looked for information about that but could not find any. Is there a way to select the canonical transcript? In my example, it is the first one starting with NM.
Or is there a list that shows the canonical transcripts of in this format (NM_). I know there is MANE but I am using hg19 for now. Also I used APPRIS but they are in Ensembl format.
Thank you in advance.
The longest CDS (coding DNA sequence) is usually the canonical transcript (http://www.ensembl.org/Help/Glossary)
Whatever API you are using, there should be a way to make the tool to select or let you know which transcript is canonical. SnpEff and VEP (probably ANNOVAR too, but not sure) have that option. Check if your tool has that option or you can shift to VEP/SnpEff/ANNOVAR.