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Clinical-Genomics / raredisease

CG's rare disease pipeline in next flow, see the main repo here 👇
https://github.com/nf-core/raredisease
MIT License
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Annotating 5'UTRs #3

Open fulyataylan opened 2 years ago

fulyataylan commented 2 years ago

Hi!

I have recently listened to an ESHG talk about annotating variants in 5'UTR. I found it very interesting and it is worth trying. Below you can find their GitHub page and publications.

https://github.com/ImperialCardioGenetics/UTRannotator

About the role of 5'UTR variants in human genetic disease:

Whiffin, N., Karczewski, K.J., Zhang, X. et al. Characterising the loss-of-function impact of 5’ untranslated region variants in 15,708 individuals. Nat Commun 11, 2523 (2020). https://doi.org/10.1038/s41467-019-10717-9

About UTRannotator:

Annotating high-impact 5'untranslated region variants with the UTRannotator Zhang, X., Wakeling, M.N., Ware, J.S, Whiffin, N. Bioinformatics; doi: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa783/5905476

Kind regards, Fulya

jemten commented 2 years ago

First of all sorry about the late reply. Indeed, this looks very interesting. We are currently in the process of rewriting MIP in nextflow which takes a lot of our resources and thus the work on MIP has been limited to maintenance mostly. However, we will try to include this in the nf-core pipeline :)

henrikstranneheim commented 2 years ago

Will not be done in MIP

jemten commented 2 years ago

Transferred this to our fork of the raredisease repo in order to not forget about it

jemten commented 9 months ago

VEP plugin available https://github.com/Ensembl/VEP_plugins/blob/release/110/UTRAnnotator.pm