snpEff annotation

[omerfaruk]

I am trying to understand genome trax download option bed and gff files.

What is the best tool for annotating vcf files with genome trax download option files formatted as bed and gff?

I tried with snpEff so far which is my choice but got no luck.

Best regards,

[bb420]

Hello

This reply comes a little late, but I hope it may still be relevant for you.
I would suggest you to check out Annovar, especially if you are using the gff files. (My impression is that you have a Genome Trax license, and want to further annotate the variants. correct me if I am wrong!). If you just want your VCFs to be called with SNPeff, you can do that independently (for things like frameshift etc), and then can add annotations using Annovar.
You can get more info on Annovar here: http://www.openbioinformatics.org/annovar/

Bhanu