markdups_gatk: Wrapper for MarkDuplicatesSpark from gatk

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

Wrapper for MarkDuplicatesSpark from gatk

Description

This function removes duplicated reads (artifacts) found in aligned sequences and sorts the output bam.

Usage

markdups_gatk(
  sif_gatk = build_default_sif_list()$sif_gatk,
  bam = "",
  output_dir = ".",
  verbose = FALSE,
  batch_config = build_default_preprocess_config(),
  tmp_dir = ".",
  threads = 3,
  ram = 4,
  remove_duplicates = TRUE,
  executor_id = make_unique_id("markdupsGATK"),
  task_name = "markdupsGATK",
  mode = "local",
  time = "48:0:0",
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

sif_gatk	Path to gatk 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	OPTIONAL Enables progress messages. Default False.#
tmp_dir	Path to tmp directory.
threads	Number of threads . Default 4
ram	RAM memory. Default 4
remove_duplicates	Remove all sequencing duplicates from BAM file. Default TRUE.
executor_id	Task EXECUTOR ID. Default "mardupsGATK"
task_name	Task name. Default "mardupsGATK"
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.

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