Annotation of SV over genes

[fritzsedlazeck]

More like a suggestion. I think it would be awesome to have this included. We could run e.g. vcfanno, which is very fast and provide the users with an annotation (in terms of gene space) together with their variants.

Most of the time people feel a bit overwhelmed with a VCF including thousands of variants. Giving them the opportunity to quickly query their gene of interest could go a long way. Thus, running vcfanno could further annotate SVs overlapping with genes.

Let me know if you need some help with that.
Cheers
Fritz

[slzarate]

OK, I think this should be doable once I've released some bug fixes. Do you foresee this being an optional field, allowing users to provide a file with which to annotate their VCF?

[fritzsedlazeck]

Yeah I would do it like that. Let me know if I can help.
Thanks
Fritz

[slzarate]

There are some feature requests I'm prioritizing before this, but yes, I will let you know once I start working on it!

[davidcotter]

Perhaps of interest, I have used AnnotSV -- (paper) on the output genotype VCF of parliament2 and it worked well. It includes gene names as well as many other annotations e.g. class "Pathogenic" etc and has binaries and all annotation DBs included is a single package.