Question: Annovar annotation for plants
0
gravatar for felipead66
6 months ago by
felipead6630
felipead6630 wrote:

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?

plants annovar • 250 views
ADD COMMENTlink modified 6 months ago by Vitis2.2k • written 6 months ago by felipead6630
1
gravatar for Vitis
6 months ago by
Vitis2.2k
New York
Vitis2.2k wrote:

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

ADD COMMENTlink written 6 months ago by Vitis2.2k
0
gravatar for Erin_Ensembl
6 months ago by
Erin_Ensembl380
EMBL-EBI
Erin_Ensembl380 wrote:

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.

ADD COMMENTlink written 6 months ago by Erin_Ensembl380

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.

ADD REPLYlink written 5 months ago by felipead6630

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?

ADD REPLYlink written 5 months ago by Erin_Ensembl380
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