How to annotate structural variants in VCF with esv/nsv identifiers

Question

[danilovkiri]

Hi!

I'm struggling with finding a way to annotate a manta structural variants VCF output with SV regions identifiers from DGV/dbVAR (esv/nsv). Direct annotation based on the exact reported chromosomal positions certainly would not work as most of the structural variants have imprecise start-end locations. I did not manage to find the desired functionality in VEP, snpeff, annovar and loads of other tools reported elsewhere. I would appreciate any information on this issue.

Thanks! Kirill

[zizigolu]

I have not used though but hope helps

https://github.com/brentp/vcfanno

[danilovkiri]

Thank you. Actually, I've come across this tool while googling but did not manage to comprehend its ability to do so. Now I do. I'll try it and post the result.

[WouterDeCoster]

vcfanno works very well, I can recommend it.

[zizigolu]

if you still need help I can help you

[always_learning]

Can you please help on this ?

Answer 1

[always_learning]

Can you please help on this ?

[zizigolu]

My SV caller has been Manta, my script does annotation on Manta. What is your SV caller?

[always_learning]

yes Its manta. Primarily I am using MANTA for that.

[zizigolu]

You may need to install Ruby

I hope this helps