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When vep starts up it looks for the tabix command. This is part of the htslib installation, and this module is automatically loaded alongside vep.
ARCC has tried testing the halpo (also see here) command, and although the command runs, we’re unable to actually generate any results due to not having a suitable data set. It does appear that a specific data set is required “input data must be a VCF containing phased genotype data for at least one individual and file must be sorted by chromosome and genomic position; no other formats are currently supported.”
Multicore:
The vep command can run across multicores, view the vep command for more details about the --fork option.
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