How can I use my own fasta and gff to annotate?

[DayTimeMouse]

Hi,

Thanks for developing this nice tool.

I'd like to use my own fasta and gff to annotate the VCF file, according to the mannual:

grep -v "#" data.gff | sort -k1,1 -k4,4n -k5,5n -t$'\t' | bgzip -c > data.gff.gz
tabix -p gff data.gff.gz
./vep -i input.vcf --gff data.gff.gz --fasta genome.fa.gz

Howerver, the output is variant_effect_output.txt, is not VCF file, how can I get the annotated VCF file?

Versions:
  ensembl              : 112.7104005
  ensembl-funcgen      : 112.be19ffa
  ensembl-io           : 112.2851b6f
  ensembl-variation    : 112.4113356
  ensembl-vep          : 112.0

Best regards.

[jamie-m-a]

Hi @DayTimeMouse

You can use the --vcf option to output in VCF format. Please see here for more details.