I am using VEP (v103) to annotate a small vcf file (~1000 variants). Nonetheless, it takes very long (>20 minutes) , which doesnt quite match their description of:
Set up correctly, VEP is capable of processing around 3 million variants in 30 minutes
Furthermore, it seems like the
--fork does not really work, because the whole time just one cores is used.
This is the command that i used:
vep --cache --dir_cache vep-cache --offline --fasta ref-genome.fa --pick --fork 4 --sift b --variant_class -i somatic.filtered.snp.vcf -o snp_vep_out.txt
Id be very thankful if someone could point out what I am doing wrong.