insertsize_metrics_bam_picard: Generate BAM Insert Size Metrics

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

Generate BAM Insert Size Metrics

Description

Generate BAM Insert Size Metrics

Usage

insertsize_metrics_bam_picard(
  bin_picard = build_default_tool_binary_list()$bin_picard,
  bam = "",
  output_dir = ".",
  verbose = FALSE,
  batch_config = build_default_preprocess_config(),
  tmp_dir = ".",
  threads = 1,
  ram = 4,
  mode = "local",
  executor_id = make_unique_id("insertsizeMetrics"),
  task_name = "insertsizeMetrics",
  time = "48:0:0",
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

bin_picard	Path to bwa executable. Default path tools/samtools/samtools.
bam	Path to the input file with the sequence.
output_dir	Path to the output directory.
verbose	Enables progress messages. Default False.
tmp_dir	Path to TMP directory. Default .
ram	RAM memory to use in GB. Default 4.
executor_id	OPTIONAL Task executor name. Default "recalCovariates"
task_name	OPTIONAL Task name. Default "recalCovariates"
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.