new_sort_and_index_bam_samtools: Sort and index a sequence 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

Sort and index a sequence file

Description

Wrapper around index_bam_samtools and sort_bam_samtools functions

Usage

new_sort_and_index_bam_samtools(
  bin_samtools = build_default_tool_binary_list()$bin_samtools,
  bam = NULL,
  sort = TRUE,
  index = TRUE,
  coord_sort = TRUE,
  stats = TRUE,
  ...
)

Arguments

bin_samtools	Path to samtools executable. Default path tools/samtools/samtools.
bam	Path to the input file with the sequence.
sort	Sort BAM file. Default TRUE.
index	Generate an index file for sorted BAM. Default TRUE
coord_sort	Generate a coord sorted file. Otherwise queryname sorted. Default TRUE
stats	Generate BAM stats. Default all. Options "all","flag","index",""
output_dir	Path to the output directory.
verbose	Enables progress messages. Default False.
threads	Number of threads. Default 3
ram	Ram memory to use per thread in GB. Default 1GB
clean	Remove input files. Default FALSE
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.
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.