panel_of_normals_ichorCNA: Generate panel of normals for ichorCNA

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 panel of normals for ichorCNA

Description

This function generates a report that helps to segment the genome, predict large-scale copy number alterations, and estimate tumor fraction in ULP-WGS samples.

Usage

panel_of_normals_ichorCNA(
  bin_ichor_pon = build_default_tool_binary_list()$bin_ichor_pon,
  wigs_dir = "",
  wigs = "",
  bed = "",
  output_name = "PoN_ichorCNA",
  gc = "tools/ichorCNA/inst/extdata/gc_hg19_500kb.wig",
  map = "tools/ichorCNA/inst/extdata/map_hg19_500kb.wig",
  centromere = "tools/ichorCNA/inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt",
  male_tresh = 1e-04,
  verbose = TRUE
)

Arguments

bin_ichor_pon	Path to ichorCNA executable. Default path tools/ichorCNA/scripts/createPanelOfNormals.
wigs_dir	Path to dir with WIG files.
wigs	Path to the WIG files.
bed	Path to BED file with target regions.
output_name	File output name.
gc	Path to GC-content WIG with . Default tools/ichorCNA/inst/extdata/gc_hg19_500kb.wig
map	Path to mappability score WIG with GC content. Default tools/ichorCNA/inst/extdata/map_hg19_500kb.wig
centromere	Path to file containing centromere locations. Default tools/ichorCNA/inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt
male_tresh	Minimum percentage of reads in chromosome Y to call male. Default 0.0001
verbose	Enables progress messages. Default False.
output_dir	Path to the output directory.

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