run_samtools: Run Samtools

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

Run Samtools

Description

Runs the samtools program

Usage

run_samtools(
  command = NULL,
  input = NULL,
  output = NULL,
  threads = 10,
  mapq = NULL,
  memory = "5G",
  parallel = FALSE,
  cores = 4,
  execute = TRUE,
  samtools = NULL,
  version = FALSE
)

Arguments

command	Samtools command to run, at present can choose from 'view', 'sort', 'index' and 'depth', required
input	List of aligned files in sam or bam format, required
output	List of file names for output,
threads	Number of threads for samtools to use, default set to 10
mapq	Set to minimum mapping quality, for filtering bam files
memory	Set maximum memory per thread, default set to 5Gb
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
samtools	Path to the samtools program, required
version	Returns the version number

Value

A list with the samtools commands

Examples

## Not run: 
alignments_path <- "hisat2_alignments"
sam.files <- list.files(path = alignments_path, pattern = "sam$",
                       full.names = TRUE, recursive = TRUE)
bam.files <- gsub(sam.files, pattern = ".sam", replacement = ".bam")
sorted.bam.files <- gsub(sam.files, pattern = ".sam", replacement = "_sorted.bam")
sample_names <- unlist(lapply(strsplit(list.files(path = reads_path,
                       pattern = "*_R1_001.fastq$",
                       full.names = FALSE),"_"), `[[`, 1))

command <- "view"
samtools.cmds <- run_samtools(command = command,
                              input = sam.files,
                              output = bam.files,
                              sample.name = sample_names
                              samtools = samtools.path))
samtools.cmds

command <- "sort"
samtools.cmds <- run_samtools(command = command,
                              input = bam.files,
                              output = sorted.bam.files
                              samtools = samtools.path)
samtools.cmds

command <- "index"
samtools.cmds <- run_samtools(command = command,
                              input = sorted.bam.files,
                              samtools = samtools.path)
samtools.cmds
command <- "depth"
samtools.cmds <- run_samtools(command = command,
                              input = sorted.bam.files,
                              output = outfile.names,
                              samtools = samtools.path)
samtools.cmds

## End(Not run)

GrahamHamilton/pipelineTools documentation built on Aug. 4, 2024, 3:18 a.m.