run_picard: Run Picard

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

Run Picard

Description

Runs the Picard program. Curently only works for CollectRnaSeqMetrics, CollectWgsMetrics & MarkDuplicates command

Usage

run_picard(
  command = NULL,
  input = NULL,
  output = NULL,
  out.dir = NULL,
  refFlat = NULL,
  reference = NULL,
  rRNA.intervals = NULL,
  intervals = NULL,
  strand = NULL,
  remove.duplicates = FALSE,
  sample.name = NULL,
  library = NULL,
  platform = NULL,
  unit = NULL,
  vcf.files = NULL,
  parallel = FALSE,
  cores = 4,
  execute = TRUE,
  picard = NULL
)

Arguments

command	Picard command to run, required
input	List of sorted bam files, required
output	List of output bam files, required for MarkDuplicates command
out.dir	Name of the output directory, required
refFlat	Path to the refFlat file, required for CollectRnaSeqMetrics commmand
reference	Path to the fasta formatted reference for CollectWgsMetrics command
rRNA.intervals	Path to the rRNAintrvals list file
intervals	Path to the intrvals list file, usually the exome coordiantes file
strand	Strand-specific information, "FR" for first strand or "RF" for reverse strand, required for CollectRnaSeqMetrics commmand
remove.duplicates	Set for removing marked duplicates, boolean default set to FALSE
sample.name	List of the sample names, required
library	Read group library
platform	Sequencing platform, e.g. ILLUMINA
unit	Platform unit, e.g. run barcode or number
vcf.files	List of VCF files to sort and merge
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
picard	Path to the Picard program, required

Value

A list with the Picard commands

Examples

## Not run: 
sorted.bam.files <- list.files(path = hisat2.alignments.dir, pattern = "sorted.bam$",
                               full.names = TRUE, recursive = TRUE)
sample_names <- unlist(lapply(strsplit(list.files(path = trimmed_reads_dir,
                       pattern = "*_R1_001.fastq$",
                       full.names = FALSE),"_"), `[[`, 1))
picard.dir <- "picard"
refFlat.file <- "refFlatBDGP6.txt"

run_picard(command = "CollectRnaSeqMetrics",
           input = sorted.bam.files,
           out.dir = picard.dir,
           refFlat = refFlat.file,
           strand = strandedness,
           sample.name = sample.names,
           picard = picard.path)

## End(Not run)

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