mapq_metrics_bam_samtools: Generate BAM MapQ 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 MapQ metrics

Description

Generate BAM MapQ metrics

Usage

mapq_metrics_bam_samtools(
  bin_samtools = build_default_tool_binary_list()$bin_samtools,
  bam = "",
  output_dir = ".",
  verbose = FALSE,
  batch_config = build_default_preprocess_config(),
  threads = 3,
  ram = 4,
  mode = "local",
  executor_id = make_unique_id("metricsMAPQ"),
  task_name = "metricsMAPQ",
  time = "48:0:0",
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

bin_samtools	Path to samtools 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.
threads	Number of threads. Default 3
mode	REQUIRED Where to parallelize. Default local. Options "local","batch"
executor_id	Job EXECUTOR ID. Default "mardupsGATK"
task_name	Name of the task. Default "mardupsGATK"
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.