run_freebayes: Run Freebayes

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

Run Freebayes

Description

Run Freebayes

Usage

run_freebayes(
  input = NULL,
  list = NULL,
  reference = NULL,
  output = NULL,
  targets = NULL,
  ploidy = NULL,
  parallel = FALSE,
  cores = 4,
  execute = TRUE,
  freebayes = NULL,
  version = FALSE
)

Arguments

input	List of aligned bam files
list	File with a list of bam files
reference	Reference genome sequence in fasta format
output	List of file names for out put
targets	Limit analysis to targets listed in the BED-formatted file
ploidy	Sets the default ploidy for the analysis, default st to 2
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
freebayes	Path to the freebayes program, required
version	Returns the version number

Value

A list of freebayes commands

Examples

## Not run: 
 freebayes <- "/usr/bin/freebayes"

 freebayes.verion <- run_freebayes.1(freebayes = freebayes,
                                   version = TRUE)

 freebayes.cmds <- run_freebayes(input = "input.bam",
                                 reference = "reference.fa",
                                 output = "out.vcf",
                                 ploidy = 2,
                                 execute = FALSE,
                                 freebayes = freebayes)

## End(Not run)

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