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)

Arguments

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

Examples

vep(debug = TRUE)
#> vep --cache_version 91 --assembly GRCh37 --dir /Users/ljf/.vep --output_file variant_effect_output.txt --cache --offline --everything
#> [1] "vep --cache_version 91 --assembly GRCh37 --dir /Users/ljf/.vep --output_file variant_effect_output.txt --cache --offline --everything "