I am trying to annotate WGS VCF files through VEP, and even on multi-threading (n=8) the process is painfully slow. The VCF sizes range between 1-1.5Gb. Around 2 days for each VCF
What would you recommend to speed up the process? I can break the VCF into chunks. Any other sol. or software reco.? Apart from gene & functional impact level anno., I am using VEP plugins for CADD and gnomAD genome based freq.