index_bam_samtools: Index a BAM file

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

Index a BAM file

Description

This function sorts a genome sequence file (BAM/SAM)

Usage

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

Arguments

bam	Path to the input file with the sequence.
verbose	Enables progress messages. Default False.
threads	Number of threads. Default 3
ram	Ram memory to use per thread in GB. Default 1GB
mode	REQUIRED Where to parallelize. Default local. Options "local","batch"
executor_id	Task 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.
output_dir	Path to the output directory.
wait	OPTIONAL If batch mode wait for batch to finish. Default FALSE
hold	OPTIONAL Hold job until job is finished. Job ID.
bin_samtols	Path to samtools executable. Default path tools/samtools/samtools.
coord_sort	Generate a coord sorted file. Otherwise queryname sorted. Default TRUE
clean	Remove input files. Default FALSE

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