Does annovar print canonical transcripts?
1
2
Entering edit mode
6.1 years ago
agata88 ▴ 840

Hi all,

Does annovar have an option to print only canonical transcripts? Or should I just select from all printing NM numbers?

And if so, how can I obtain only NM numbers for canonical transcripts? e.g from UCSC? (I don't need chr, chrstart, chrend, geneID etc.)

Maybe somebody already has some kind of list and would like to share? :)

Thanks in advance,

Agata

annovar transcripts • 1.9k views
ADD COMMENT
0
Entering edit mode

i think it do .. but try the new version

ADD REPLY
1
Entering edit mode
5.7 years ago
steve ★ 3.1k

From the documentation:

http://annovar.openbioinformatics.org/en/latest/misc/faq/

Why ANNOVAR reports T182A,T190A,T300A as the amino acid change but another web server reports only T300A?
Alternative splicing is prevalent in human genome and as a result, it is best to annotate amino acid change with respect to a certain transcript rather than gene. Other servers or software may randomly pick one script as the representative "gene" and gives one single answer. ANNOVAR tries to be comprehensive and always accompany annotation by transcript names, and it is up to the user which representative transcript they want to use or if they want to use all. There has never been a concensus in the field which transcript should be used to represent a gene when multiple transcripts are available. The most popular approach is to use the longest transcript nowadays. However, in the medical genetics field, for certain specific diseases and specific genes, there are 'canonical' transcripts that everybody uses by default for historical reasons, and you will need to manually select this canonical transcript from ANNOVAR output file to communicate with the rest of the field.

I am interested in the same thing though, so I would love to hear about any solutions others may have for this.

ADD COMMENT

Login before adding your answer.

Traffic: 1770 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6