Hi I am trying to annotate the variants in a vcf file using snpEFF, but its giving multiple annotations for a single position. Any suggestions on how to choose the best or most appropriate one?
Thanks in advance
Firstly, I'd suggest checking some of the results with another annotation tool. Perhaps get a few of those variants giving multiple annotations and confirm the pattern with the rather popular and powerful Variant Effect Predictor, or VEP. As suggested already in the comments here, the multiple annotation will be due to alternatively splicing and there is nothing much we can do apart from trying to chose one or a few "best" ones based on certain parameters and based on the question you want to answer, really. Let's suppose you are interested in the most severe consequence of a given variant. If so, choose the most severe consequence with the VEP(--most_severe flag). If you want to focus on the reliability of a transcript, you can pick the annotations for Ensembl genes that are golden (identical annotation between Ensembl and HAVANA). You can also filter out those that have lower TSL (use the --tsl flag on the VEP script) or choose the 'canonical' (find out what is deemed as canonical transcript by Ensembl) transcript (use the --canonical flag), and so on so forth...
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
version 2.3.6
life... again...
use the "worst" one. e.g: non-synonymous > synonymous. But it depends of your needs...
and the context. For example, the example you provided will most probably only be seen with alternative splicing or multiple reading frames. I wonder how one picks the best fit annotation without falling into the cherry-picking conundrum.
Exactly, I was wondering whether there is a way to figure this out as I have to parse almost 100 vcf files so that I can write a script?
Not really. Scripts can automate monotonous tasks, but they cannot do stuff that need subjective perspectives - not basic tools at least.