sliding_bin_genome: Function to bin chromosome across_sliding windows

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

Function to bin chromosome across_sliding windows

Description

This function takes a FAI/ BAM file and generates a bed file with the binned regions

Usage

sliding_bin_genome(
  bin_samtools = build_default_tool_binary_list()$bin_samtools,
  file = NULL,
  output_name = "chrReference",
  bin_size = NULL,
  step_size = NULL,
  output_dir = ".",
  header = TRUE,
  verbose = FALSE,
  batch_config = build_default_preprocess_config(),
  executor_id = make_unique_id("binGenome"),
  task_name = "binGenome",
  mode = "local",
  time = "48:0:0",
  threads = 4,
  ram = 4,
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

file	Path to directory with fasta file.
output_name	Output name
bin_size	Average bin size. Defaul NULL.
header	Create column header. Default TRUE
verbose	OPTIONAL Enables progress messages. Default False.#
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"
threads	Number of threads . Default 4
ram	RAM memory. Default 4
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.
n_bins	Number of bins. Defaul NULL.

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