run_snpeff: Run SnpEff

In GrahamHamilton/pipelineTools: Pipeline Tools for NGS Sequence Analysis Pipelines

Run SnpEff

Description

Runs the SnpEff program.

Usage

run_snpeff(
  command = NULL,
  input = NULL,
  output = NULL,
  genome = NULL,
  config = NULL,
  parallel = FALSE,
  cores = 4,
  execute = TRUE,
  snpeff = NULL,
  version = FALSE
)

Arguments

command	SnpEff command to run
input	Input file, vcf format
output	Name of output file, vcf format
genome	Name of the genome
config	Path to the configuration file
parallel	Run in parallel, default set to FALSE
cores	Number of cores/threads to use for parallel processing, default set to 4
execute	Whether to execute the commands or not, default set to TRUE
snpeff	Path to the SnpEff program, required
version	Returns the version number

Value

A list with the snpEff commands

Examples

## Not run: 
 snpeff.path <- "/software/snpEff-v5.0e/snpEff.jar"

 # Version
 res <- run_snpeff(snpeff = snpeff.path,
                   version = TRUE)

 # Download a premade genome
 command <- "download"
 genome <- "GRCh38.99"

 res <- run_snpeff(command = command,
                   genome = genome,
                   execute = FALSE,
                   snpeff = snpeff.path)

 # Run snpEff
 res <- run_snpeff(command = command,
                   genome = genome,
                   input = "input.vcf",
                   output = "annotated.vcf",
                   execute = FALSE,
                   snpeff = snpeff.path)

## End(Not run)

GrahamHamilton/pipelineTools documentation built on Dec. 8, 2024, 3:53 p.m.