Tools for detection of variants in near-coding regions

[fulyataylan]

Hi!

I am opening my previous ticket again! Once more I listened to some talks in ESHG Vienna and I believe we should have these tools implemented in our analysis pipelines.

As I mentioned previously, 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

Other tools that are useful if still not in use:
SpliceAI: https://github.com/Illumina/SpliceAI

This is super interesting and should be added to the pipeline:
https://github.com/edg1983/GREEN-VARAN

Probably a useful tool for SV analysis and visualization:
https://github.com/Oxford-Eye/SVRare-db
https://github.com/Oxford-Eye/SVRare-js
https://github.com/Oxford-Eye/SVRare-GEL

To detect splicing variants:
https://github.com/jpaggi/labranchor

These are the tools that are mainly used in Genomics England and presented at ESHG this year.

Kind regards,
Fulya

Fulya Taylan
KI, Rare Diseases

[jemten]

Hi Fulya!
Thanks for the tools suggestions!
We run SpliceAI in MIP currently so those annotations should be available to you already but the we need to add the rest. We'll look into adding these tools in the new nextflow pipeline 😄