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, https://github.com/Ensembl/ensembl-vep). In that page it says that for a custom annotation and fasta you can use:
perl vep.pl -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.
Given the lack of reply here, you may want to create an issue on GitHub as suggested in their README.
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).
You can also try variant_effect_predictor.pl from Ensembl (the antecesor of VEP). You can build a "cache" by providing a GFF and the reference genome sequence. Then you can run variant_effect_predictor.pl specifying that cache. This worked for me.