Question: tools for variant annotations
0
gravatar for world_genesis
2.4 years ago by
world_genesis0 wrote:

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

variant annotations tools • 2.1k views
ADD COMMENTlink modified 11 months ago by slcrick180 • written 2.4 years ago by world_genesis0
1

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.

ADD REPLYlink written 2.4 years ago by h.mon28k

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.

ADD REPLYlink written 2.4 years ago by world_genesis0
1
gravatar for slcrick
11 months ago by
slcrick180
United States
slcrick180 wrote:

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

ADD COMMENTlink modified 11 months ago • written 11 months ago by slcrick180

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?

ADD REPLYlink written 11 months ago by genomax75k

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.

ADD REPLYlink written 11 months ago by slcrick180
1

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.

ADD REPLYlink modified 11 months ago • written 11 months ago by genomax75k

Thanks. I'll try it!

ADD REPLYlink written 11 months ago by slcrick180
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