replace_rg: Wrapper around samtools addreplacerg function

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

Wrapper around samtools addreplacerg function

Description

This functions add/replaces RG tags lines in BAM files This function wraps around samtools addreplacerg function

Usage

replace_rg(
  bin_samtools = build_default_tool_binary_list()$bin_samtools,
  bam = "",
  output_dir = ".",
  verbose = FALSE,
  batch_config = build_default_preprocess_config(),
  index = TRUE,
  ID = "",
  PL = "",
  PU = "",
  LB = "",
  SM = "",
  threads = 3,
  jobs = 1
)

Arguments

bin_samtools	REQUIRED Path to santools binary. Default tools/samtools/samtools.
bam	REQUIRED Path to the BAM file/s.
output_dir	OPTIONAL Path to the output directory.
verbose	OPTIONAL Enables progress messages. Default False.
index	OPTIONAL Generate an indexed file. Default False.
ID	REQUIRED ID tag for RG tag line.
PL	OPTIONAL PL tag for RG tag line.
PU	OPTIONAL PU tag for RG tag line.
LB	OPTIONAL LB tag for RG tag line.
SM	OPTIONAL SM tag for RG tag line.
threads	OPTIONAL Number of threads per jobs.
jobs	OPTIONAL Number of jobs to run.

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