Annovar annotation for plants

Question

[felipead66]

I want to annotate .vcf files generated with gatk for prunus dulcis genome https://www.rosaceae.org/analysis/295

I cannot figure out how to do the annotation. Should I use files from the functional analysis? And how?

Answer 1

[Vitis]

In addition to the excellent VEP, the other option would be using SnpEff, for which you could build your custom annotation database with GTF or GFF3 and annotate the VCFs. For details see:

http://snpeff.sourceforge.net/SnpEff.html

Answer 2

[Erin Haskell | ELIXIR]

Not sure about annovar, but you can use Ensembl's variant effect predictor (VEP) offline tool with any species as long as you have the fasta file and the GTF gene annotation file, which appear to be available on the link you posted.

[felipead66]

I did run VEP but as a consequence i only get "intergenic_variants".

I assume something is wrong with the entire run but I cannot figure out what.

[Erin Haskell | ELIXIR]

I suspect that it might be a problem with the gene annotation file (GTF) being recognised. Can you send an email to Helpdesk [at]ensembl.org so we can take a look in more detail?