Running VEP with GTF files

The Variant Effect Predictor (VEP) is a popular tool for annotating genetic variants and it seems like has been around forever. Typically, running VEP requires the use of a cache file, which is a downloadable file containing transcript models and other features requried for variant annotation.

Well, I was today years old when I realized that VEP can also be run with GTF files. This is a great option for those who want to run VEP without downloading the cache file.

I pulled down Gencode GTF files for human here.

I have a Nextflow process for running VEP with GTF files here

But the basic command is:

vep -i ${phased_vcf} -o ${sample_id}.deepvariant.phased.vep.vcf.gz --format vcf --gtf ${pigeon_gtf} --fasta ${reference} --vcf --everything --fork 8 --compress_output bgzip

Even after using a VEP for many years, there is always something new to learn!