vep: Vairant Effect Predictor (VEP)

In omicsCore/SEQprocess: SEQprocess : a modularized and customizable pipeline framework for NGS processing in R package.

Description

A wrapper function to run VEP

Usage

vep(fns.vcf, output.dir, sample.name, perl5.10.path="/usr/bin", vep.db.dir, run.cmd=TRUE, mc.cores=1)

Arguments

fns.vcf	Path to VCF files
output.dir	Output directory
vep.db.dir	Specify the cache directory to use.
perl5.10.path	Absolute path to perl 5.10 version. VEP is a Perl based tool. We recommend version 5.10. (default="/usr/bin")
run.cmd	Whether to execute the command line (default=TRUE)
mc.cores	The number of cores to use. Must be at least one(default=1), and parallelization requires at least two cores.

Details

The VEP uses the coordinates and alleles in the VCF file to infer biological context for each variant including the location of each mutation, its biological consequence (frameshift/ silent mutation), and the affected genes. Variants in the VCF files are also matched to known variants from external mutation databases.

Value

text file and html file included variant information

References

The Ensembl Variant Effect Predictor

See Also

https://asia.ensembl.org/info/docs/tools/vep/script/vep_options.html

omicsCore/SEQprocess documentation built on May 7, 2020, 4:18 a.m.