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??