vep: R function to run VEP
In JhuangLab/annovarR: Integrated Framework to Annotate Genetic Variants

R function to run VEP

vep(
  vep = Sys.which("vep"),
  cache = TRUE,
  cache_version = 91,
  offline = TRUE,
  buildver = "GRCh37",
  dir = file.path(Sys.getenv("HOME"), ".vep"),
  input.file = "",
  out = "variant_effect_output.txt",
  fasta = "",
  everything = TRUE,
  extra.params = "",
  debug = FALSE
)

`vep`	Executable file of vep
`cache`	Enables use of the cache. Add –refseq or –merged to use the refseq or merged cache, (if installed).
`cache_version`	Use a different cache version than the assumed default (the VEP version). This should be used with Ensembl Genomes caches since their version numbers do not match Ensembl versions. For example, the VEP/Ensembl version may be 88 and the Ensembl Genomes version 35. Not used by default
`offline`	Enable offline mode. No database connections will be made, and a cache file or GFF/GTF file is required for annotation. Add –refseq to use the refseq cache (if installed). Not used by default
`buildver`	Select the assembly version to use if more than one available. If using the cache, you must have the appropriate assembly's cache file installed. If not specified and you have only 1 assembly version installed, this will be chosen by default. Default = use found assembly version (GRch37)
`dir`	Specify the base cache/plugin directory to use. Default = '$HOME/.vep/'
`input.file`	Input file name. If not specified, the script will attempt to read from STDIN.
`out`	Output file name. The script can write to STDOUT by specifying STDOUT as the output file name - this will force quiet mode. Default = 'variant_effect_output.txt'
`fasta`	Specify a FASTA file or a directory containing FASTA files to use to look up reference sequence. The first time you run the script with this parameter an index will be built which can take a few minutes. This is required if fetching HGVS annotations (–hgvs) or checking reference sequences (–check_ref) in offline mode (–offline), and optional with some performance increase in cache mode (–cache). See documentation for more details. Not used by default
`everything`	Shortcut flag to switch on all of the following: –sift b, –polyphen b, –ccds, –uniprot, –hgvs, –symbol, –numbers, –domains, –regulatory, –canonical, –protein, –biotype, –uniprot, –tsl, –appris, –gene_phenotype –af, –af_1kg, –af_esp, –af_gnomad, –max_af, –pubmed, –variant_class
`extra.params`	Extra paramters in vep command
`debug`	If set TRUE, only print the command