run_vcf_index: Compress and index vcf files

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

Compress and index vcf files

Description

Compress and index vcf files

Usage

run_vcf_index(
  input = NULL,
  type = NULL,
  parallel = FALSE,
  cores = 4,
  execute = TRUE,
  bgzip = NULL,
  tabix = NULL
)

Arguments

input	List of vcf files to index
type	File type for indexing, e.g. "vcf"
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
bgzip	Path to the bgzip program, required
tabix	Path to the tabix program, required

Value

A list with the indexing commands

Examples

## Not run: 
bgzip.path <- "/software/htslib-1.9/bin/bgzip"
tabix.path <- "/software/htslib-1.9/bin/tabix"

vcf.files <- c("file1.vcf","file2.vcf")

file.type <- "vcf"

index.vcf.cmds <- run_vcf_index(input = vcf.files,
                                type = file.type,
                                execute = FALSE,
                                bgzip = bgzip.path,
                                tabix = tabix.path)

## End(Not run)

GrahamHamilton/pipelineTools documentation built on March 5, 2024, 12:23 p.m.