ichor_wgs: Generate a ichorCNA for WGSd

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 ichorCNA for WGSd

Description

This function generates a WIG file.

Usage

ichor_wgs(
  bin_ichorcna = build_default_tool_binary_list()$bin_ichor,
  wig = NULL,
  patient_id = NULL,
  normal = "\"c(0.5,0.6,0.7,0.8,0.9)\"",
  ploidy = "\"c(2,3)\"",
  maxCN = 5,
  gcWig = build_default_reference_list()$HG19$wgs$ichorcna$gc_500k,
  mapWig = build_default_reference_list()$HG19$wgs$ichorcna$map_500k,
  centromere = build_default_reference_list()$HG19$wgs$ichorcna$centromere,
  normalPanel = build_default_reference_list()$HG19$wgs$ichorcna$pon_500k,
  chrs = "\"c(1:22, 'X')\"",
  chrTrain = "\"c(1:22)\"",
  estimateNormal = TRUE,
  estimatePloidy = TRUE,
  estimateScPrevalence = TRUE,
  includeHOMD = FALSE,
  scStates = "\"c(1,3)\"",
  txnE = 0.9999,
  txnStrength = 10000,
  ...
)

Arguments

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