Annotation of delly (and other SV caller) output

[Maximus Yeung]

Hello everyone,

After getting the output from Delly (and other SV caller), may I know how I get do annotation for further downstream analysis?

Specificially I want to know what gene is involved, which exon/intron has been involved in translocation, what will be expected fusion transcript, what is the functional significance of the fusion protein, etc.

Thanks a lot!

[Damian Loska]

I use Ensembl's VEP. It works nice directly with the vcf generated by delly.

I didn't try this yet: https://exomiser.readthedocs.io/en/latest/sv_prioritisation.html 

I'd be happy to learn other tools that may be usefule in using/intepreting/parsing delly's outputs.