run_vcftools: Run vcftools

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

Run vcftools

Description

Runs the vcftool, currently only set for creating PLINK Map and Ped files

Usage

run_vcftools(
  input = NULL,
  output = NULL,
  plink = FALSE,
  execute = TRUE,
  vcftools = NULL,
  version = NULL
)

Arguments

input	Path to the input vcf file
output	Path to the output files
plink	Create plink files, boolean, default st to FALSE
execute	Whether to execute the commands or not, default set to TRUE
vcftools	Path to the vcftools program, required
version	Returns the version number

Value

Alist of vcftools commnads

Examples

## Not run: 
vcftools.path <- "/software/vcftools-v0.1.16/bin/vcftools"

run_vcftools(vcftools = vcftools.path,
             version = TRUE)

input.file <- "variants.vcf"
output.file <- gsub("vcf","plink",input.file)

run_vcftools(input = input.file,
             output = output.file,
             plink = TRUE,
             execute = FALSE,
             vcftools = vcftools.path)

## End(Not run)

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