markdups_picard: Mark duplicated reads

In TearsWillFall/ULPwgs: An implementation of a wrapper for estimating tumor fraction in ultra-low-pass whole genome sequencing (ULP-WGS) for cell-free DNA in GNU/Unix based systems

Mark duplicated reads

Description

This function marks duplicated reads (artifacts) found in aligned sequences.

Usage

markdups_picard(
  bin_picard = build_default_tool_binary_list()$bin_picard,
  bam = "",
  output_dir = ".",
  verbose = FALSE,
  batch_config = build_default_preprocess_config(),
  hnd = 1000,
  threads,
  ram = 4,
  tmp_dir = ".",
  remove_duplicates = TRUE,
  mode = "local",
  executor_id = make_unique_id("markDups"),
  task_name = "markDups",
  time = "48:0:0",
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

bin_picard	Path to picard executable. Default path tools/picard/build/libs/picard.jar.
bam	Path to the input file with the aligned sequence.
output_dir	Path to the output directory.
verbose	Enables progress messages. Default False.
hnd	Maximum number of file handles. Default 1000.
tmp_dir	Path to tmp directory.
remove_duplicates	Do not write duplicates to the output file. Default FALSE
mode	REQUIRED Where to parallelize. Default local. Options "local","batch"
time	OPTIONAL If batch mode. Max run time per job. Default "48:0:0"
update_time	OPTIONAL If batch mode. Job update time in seconds. Default 60.
wait	OPTIONAL If batch mode wait for batch to finish. Default FALSE
hold	OPTIONAL HOld job until job is finished. Job ID.
executor	OPTIONAL Task executor name. Default "recalCovariates"
task	OPTIONAL Task name. Default "recalCovariates"

TearsWillFall/ULPwgs documentation built on April 18, 2024, 3:45 p.m.