tools for variant annotations

Question

[world_genesis]

Which are the lesser known tools for variant annotations which specifically have VCF as input file format?

[h.mon]

Which are the greater known tools for variant annotation that you do know specifically?

I know of VEP, Annovar, SnpEff and SnpSift, VariantAnnotation.

They are not probably lesser known, but one never knows how much someone else knows. If I unknowingly offended you with my list, please let me know. The WikiPedia page on SNP annotation has a long list, however, as they are on WikiPedia, they probably are not the lesser known ones as well.

[world_genesis]

I asked for the "lesser" known ones since I did not want to miss out any from my list. The ones mentioned by you are common ones which even a simple Google search could have told me.

Answer 1

[slcrick]

open-cravat handles VCF input file format. Disclosure: I am the lead architect of open-cravat.

[GenoMax]

When referring to a package it is customary to include links. Multiple packages can have similar names. I think you are referring to this package?

[slcrick]

Yes, sorry I am still new to Biostars and thought that if it might be prohibited to include a link to the software with which a commenter himself/herself is involved.

[GenoMax]

That is fine to do since you are not a commercial entity selling software. You could create a separate post describing your software under tools category (if it has not been described on biostars before). You can see some examples here. With the inclusion of correct tag you can even follow threads that ask questions about a particular tag.

[slcrick]

Thanks. I'll try it!