Question: Variant Effect Predictor parameters for custom gff and fasta
gravatar for R.Blues
3.8 years ago by
R.Blues130 wrote:

Hello everyone,

I am learning to use Ensemble VEP (Variant Effect Predictor) in command line mode. I am interested in predicting the effect of variants in an not-standard genome, with my own annotation.

I am using the VEP Github pre-release version (it is a new version, In that page it says that for a custom annotation and fasta you can use:

perl -i input.vcf -gff data.gff.gz -fasta genome.fa.gz

This is not working for me (it has an error when inferring the transcripts from the GFF). If I do it as with the earlier VEP versions for a custom GFF ("-custom myFeatures.gff.gz,myFeatures,gff,overlap,0"), it creates an output, but I have the impression that this output does not use the fasta file for anything (if I remove the " -fasta genome.fa.gz" option, I obtain the same results).

So I am a bit clueless (there is a lot of information, but I have not found enough information for this case). How should I input these parameters? What am I doing wrong??

Thank you.

snp vep gff fasta • 1.7k views
ADD COMMENTlink modified 2.4 years ago by nicolas.dussex30 • written 3.8 years ago by R.Blues130

Given the lack of reply here, you may want to create an issue on GitHub as suggested in their README.

ADD REPLYlink written 3.8 years ago by Denise CS5.1k

CooVar was developed for annotating non-standard genomes. The paper contains an in-depth comparison with VEP results. (Disclaimer: I'm co-author of this paper).

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by Christian2.9k

You can also try from Ensembl (the antecesor of VEP). You can build a "cache" by providing a GFF and the reference genome sequence. Then you can run specifying that cache. This worked for me.

ADD REPLYlink written 3.8 years ago by abascalfederico1.1k
gravatar for nicolas.dussex
2.4 years ago by
New Zealand
nicolas.dussex30 wrote:

Hi R.Blues,

Did you manage to fix your issue? I am trying to do the same but I am having issues creating the cache and I think that it is due to the fact that my annotation has gene, mRNA, CDSs but not exons.

Cheers, Nic

ADD COMMENTlink written 2.4 years ago by nicolas.dussex30
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