read_counter_region: Generate a WIG 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

Generate a WIG file

Description

This function generates a WIG file.

Usage

read_counter_region(
  bin_readcount = build_default_tool_binary_list()$bin_readcount,
  bam = NULL,
  region = NULL,
  win = 5e+05,
  mapq = 20,
  format = "wig",
  ...
)

Arguments

bin_readcount	Path to readCounter executable. Default path tools/hmmcopy_utils/bin/readCounter.
bam	Path to the BAM file .
win	Size of non overlaping windows. Default 500000.
format	Output format wig/seg . Default wig
bin_samtools	Path to readCounter executable. Default path tools/samtools/samtools.
output_dir	Path to the output directory.
chrs	String of chromosomes to include. c()
threads	Number of threads to use. Default 3
verbose	Enables progress messages. Default False.

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